{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "f3c651fe", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:52:30.557732Z", "iopub.status.busy": "2025-03-25T03:52:30.557355Z", "iopub.status.idle": "2025-03-25T03:52:30.728865Z", "shell.execute_reply": "2025-03-25T03:52:30.728418Z" } }, "outputs": [], "source": [ "import sys\n", "import os\n", "sys.path.append(os.path.abspath(os.path.join(os.getcwd(), '../..')))\n", "\n", "# Path Configuration\n", "from tools.preprocess import *\n", "\n", "# Processing context\n", "trait = \"Rheumatoid_Arthritis\"\n", "cohort = \"GSE97475\"\n", "\n", "# Input paths\n", "in_trait_dir = \"../../input/GEO/Rheumatoid_Arthritis\"\n", "in_cohort_dir = \"../../input/GEO/Rheumatoid_Arthritis/GSE97475\"\n", "\n", "# Output paths\n", "out_data_file = \"../../output/preprocess/Rheumatoid_Arthritis/GSE97475.csv\"\n", "out_gene_data_file = \"../../output/preprocess/Rheumatoid_Arthritis/gene_data/GSE97475.csv\"\n", "out_clinical_data_file = \"../../output/preprocess/Rheumatoid_Arthritis/clinical_data/GSE97475.csv\"\n", "json_path = \"../../output/preprocess/Rheumatoid_Arthritis/cohort_info.json\"\n" ] }, { "cell_type": "markdown", "id": "bebc6cca", "metadata": {}, "source": [ "### Step 1: Initial Data Loading" ] }, { "cell_type": "code", "execution_count": 2, "id": "07e07d81", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:52:30.730172Z", "iopub.status.busy": "2025-03-25T03:52:30.730016Z", "iopub.status.idle": "2025-03-25T03:52:31.059934Z", "shell.execute_reply": "2025-03-25T03:52:31.059370Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Background Information:\n", "!Series_title\t\"RA-MAP: mapping molecular immunological landscapes in early rheumatoid arthritis and healthy vaccine recipients [Healthy Hepatitis B Vaccine Recipients]\"\n", "!Series_summary\t\"Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 vaccine recipient controls for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.\"\n", "!Series_overall_design\t\"Patients were clinically profiled for 18 months with a variety of data taken every 3 months, microarray and miRNA-sequencing was performed at baseline and six-month timepoints.\"\n", "Sample Characteristics Dictionary:\n", "{0: ['cell type: PBMCs_for_RNA', 'cell type: RNA-Tempus', 'cell type: PBMC_CD4', 'cell type: PBMC_CD8', 'cell type: PBMC_CD14'], 1: ['patientid: 26365906D406AF22FCAABEF719F246AF2B639D477F942DA36D4C4E88942E8F79', 'patientid: DE420B7DB2BE04A1FB63551BF0A978B0C46370B9B1D042841F564D3F932ECC29', 'patientid: 237CEB8CDA21A4B2EFB3B4B8920F13CCFEA42150B56FD24ABB8190F12F1E2BEE', 'patientid: 3FD266C65D42CEAAE7EA30A6B6AD6753C44FE1170260F6E9041F5973FC740056', 'patientid: 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['steroid.injections.06.months.triamcinolone..kenalog..4.triamcinolone..kenalog..4.joint.injected.06m: NA'], 447: ['steroid.injections.18.months.triamcinolone..kenalog..1.triamcinolone..kenalog..1.joint.injected.18m: NA'], 448: ['steroid.injections.12.months.triamcinolone..kenalog..1.received.triamcinolone..kenalog..1.injection.12m: NA'], 449: ['steroid.injections.12.months.triamcinolone..kenalog..1.triamcinolone..kenalog..1.joint.injected.12m: NA'], 450: ['steroid.injections.12.months.triamcinolone..kenalog..1.triamcinolone..kenalog..1.route.12m: NA'], 451: ['steroid.injections.06.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.route.06m: NA'], 452: ['steroid.injections.06.months.triamcinolone..kenalog..3.received.triamcinolone..kenalog..3.injection.06m: NA'], 453: ['steroid.injections.06.months.triamcinolone..kenalog..1.triamcinolone..kenalog..1.dose..mg..06m: NA'], 454: ['steroid.injections.06.months.triamcinolone..kenalog..4.triamcinolone..kenalog..4.route.06m: NA'], 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['medication.09.months.golimumab.golimumab.date.started.09m: NA'], 465: ['medication.09.months.golimumab.golimumab.dose..mg..09m: NA'], 466: ['medication.09.months.golimumab.golimumab.route.09m: NA'], 467: ['medication.12.months.golimumab.golimumab.route.12m: NA'], 468: ['medication.03.months.sulfasalazine.sulfasalazine.date.started.03m: NA'], 469: ['medication.03.months.sulfasalazine.sulfasalazine.frequency.03m: NA'], 470: ['medication.12.months.golimumab.golimumab.dose..mg..12m: NA'], 471: ['medication.03.months.sulfasalazine.sulfasalazine.route.03m: NA'], 472: ['medication.12.months.golimumab.golimumab.frequency.12m: NA'], 473: ['medication.12.months.golimumab.golimumab.date.started.12m: NA'], 474: ['medication.03.months.sulfasalazine.sulfasalazine.dose..mg..03m: NA'], 475: ['steroid.injections.15.months.methylprednisolone.acetate.methylprednisolone.acetate.dose..mg..15m: NA'], 476: ['steroid.injections.15.months.methylprednisolone.acetate.received.methylprednisolone.acetate.injection.15m: NA'], 477: ['steroid.injections.15.months.methylprednisolone.acetate.methylprednisolone.acetate.joint.injected.15m: NA'], 478: ['steroid.injections.18.months.methylprednisolone.1.methylprednisolone.1.joint.injected.18m: NA'], 479: ['steroid.injections.15.months.methylprednisolone.acetate.methylprednisolone.acetate.route.15m: NA'], 480: ['steroid.injections.18.months.methylprednisolone.1.received.methylprednisolone.1.injection.18m: NA'], 481: ['steroid.injections.18.months.methylprednisolone.1.methylprednisolone.1.route.18m: NA'], 482: ['steroid.injections.18.months.methylprednisolone.1.methylprednisolone.1.dose..mg..18m: NA'], 483: ['steroid.injections.09.months.methylprednisolone.2.methylprednisolone.2.joint.injected.09m: NA'], 484: ['steroid.injections.09.months.methylprednisolone.2.received.methylprednisolone.2.injection.09m: NA'], 485: ['steroid.injections.09.months.methylprednisolone.2.methylprednisolone.2.dose..mg..09m: NA'], 486: ['steroid.injections.09.months.methylprednisolone.2.methylprednisolone.2.route.09m: NA'], 487: ['steroid.injections.18.months.methylprednisolone.acetate.methylprednisolone.acetate.dose..mg..18m: NA'], 488: ['steroid.injections.09.months.methylprednisolone.acetate.2.received.methylprednisolone.acetate.2.injection.09m: NA'], 489: ['steroid.injections.09.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.joint.injected.09m: NA'], 490: ['steroid.injections.09.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.route.09m: NA'], 491: ['steroid.injections.18.months.methylprednisolone.acetate.received.methylprednisolone.acetate.injection.18m: NA'], 492: ['steroid.injections.09.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.dose..mg..09m: NA'], 493: ['steroid.injections.18.months.methylprednisolone.acetate.methylprednisolone.acetate.joint.injected.18m: NA'], 494: ['steroid.injections.18.months.methylprednisolone.acetate.methylprednisolone.acetate.route.18m: NA'], 495: ['steroid.injections.09.months.triamcinolone..kenalog..1.triamcinolone..kenalog..1.route.09m: NA'], 496: ['steroid.injections.09.months.triamcinolone..kenalog..1.triamcinolone..kenalog..1.dose..mg..09m: NA'], 497: ['steroid.injections.09.months.triamcinolone..kenalog..1.triamcinolone..kenalog..1.joint.injected.09m: NA'], 498: ['steroid.injections.09.months.triamcinolone..kenalog..1.received.triamcinolone..kenalog..1.injection.09m: NA'], 499: ['steroid.injections.06.months.dexamethasone.1.received.dexamethasone.1.injection.06m: NA'], 500: ['steroid.injections.03.months.methylprednisolone.acetate.3.methylprednisolone.acetate.3.route.03m: NA'], 501: ['steroid.injections.03.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.route.03m: NA'], 502: ['steroid.injections.03.months.methylprednisolone.acetate.2.received.methylprednisolone.acetate.2.injection.03m: NA'], 503: ['steroid.injections.03.months.methylprednisolone.acetate.4.methylprednisolone.acetate.4.route.03m: NA'], 504: ['steroid.injections.06.months.dexamethasone.2.dexamethasone.2.route.06m: NA'], 505: ['steroid.injections.06.months.dexamethasone.1.dexamethasone.1.dose..mg..06m: NA'], 506: ['steroid.injections.03.months.methylprednisolone.acetate.3.received.methylprednisolone.acetate.3.injection.03m: NA'], 507: ['steroid.injections.06.months.dexamethasone.2.dexamethasone.2.joint.injected.06m: NA'], 508: ['steroid.injections.03.months.methylprednisolone.acetate.3.methylprednisolone.acetate.3.joint.injected.03m: NA'], 509: ['steroid.injections.03.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.joint.injected.03m: NA'], 510: ['steroid.injections.06.months.dexamethasone.1.dexamethasone.1.joint.injected.06m: NA'], 511: ['steroid.injections.03.months.methylprednisolone.acetate.4.methylprednisolone.acetate.4.joint.injected.03m: NA'], 512: ['steroid.injections.06.months.dexamethasone.2.received.dexamethasone.2.injection.06m: NA'], 513: ['steroid.injections.03.months.methylprednisolone.acetate.4.received.methylprednisolone.acetate.4.injection.03m: NA'], 514: ['steroid.injections.03.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.dose..mg..03m: NA'], 515: ['steroid.injections.03.months.methylprednisolone.acetate.4.methylprednisolone.acetate.4.dose..mg..03m: NA'], 516: ['steroid.injections.06.months.dexamethasone.2.dexamethasone.2.dose..mg..06m: NA'], 517: ['steroid.injections.03.months.methylprednisolone.acetate.3.methylprednisolone.acetate.3.dose..mg..03m: NA'], 518: ['steroid.injections.06.months.dexamethasone.1.dexamethasone.1.route.06m: NA'], 519: ['medication.18.months.leflunomide.leflunomide.route.18m: NA'], 520: ['medication.18.months.leflunomide.leflunomide.dose..mg..18m: NA'], 521: ['medication.15.months.leflunomide.leflunomide.frequency.15m: NA'], 522: ['medication.15.months.leflunomide.leflunomide.date.started.15m: NA'], 523: ['medication.18.months.leflunomide.leflunomide.date.started.18m: NA'], 524: ['medication.15.months.leflunomide.leflunomide.route.15m: NA'], 525: ['medication.15.months.leflunomide.leflunomide.dose..mg..15m: NA'], 526: ['medication.18.months.leflunomide.leflunomide.frequency.18m: NA'], 527: ['subjects.medical.history.alcohol.history.units.of.alcohol.consumption.per.week..if.over.20.: NA'], 528: ['medication.18.months.etanercept.etanercept.route.18m: NA'], 529: ['medication.18.months.etanercept.etanercept.dose..mg..18m: NA'], 530: ['steroid.injections.15.months.triamcinolone..kenalog..triamcinolone..kenalog..dose..mg..15m: NA'], 531: ['steroid.injections.15.months.triamcinolone..kenalog..received.triamcinolone..kenalog..injection.15m: NA'], 532: ['medication.18.months.etanercept.etanercept.date.started.18m: NA'], 533: ['medication.18.months.etanercept.etanercept.frequency.18m: NA'], 534: ['steroid.injections.15.months.triamcinolone..kenalog..triamcinolone..kenalog..route.15m: NA'], 535: ['steroid.injections.15.months.triamcinolone..kenalog..triamcinolone..kenalog..joint.injected.15m: NA'], 536: ['steroid.injections.18.months.methylprednisolone.2.methylprednisolone.2.route.18m: NA'], 537: ['medication.15.months.etanercept.etanercept.route.15m: NA'], 538: ['steroid.injections.15.months.methylprednisolone.1.received.methylprednisolone.1.injection.15m: NA'], 539: ['medication.15.months.etanercept.etanercept.date.started.15m: NA'], 540: ['steroid.injections.15.months.methylprednisolone.1.methylprednisolone.1.route.15m: NA'], 541: ['steroid.injections.18.months.methylprednisolone.2.methylprednisolone.2.dose..mg..18m: NA'], 542: ['steroid.injections.15.months.methylprednisolone.1.methylprednisolone.1.joint.injected.15m: NA'], 543: ['steroid.injections.18.months.methylprednisolone.2.methylprednisolone.2.joint.injected.18m: NA'], 544: ['steroid.injections.15.months.methylprednisolone.1.methylprednisolone.1.dose..mg..15m: NA'], 545: ['medication.12.months.etanercept.etanercept.date.started.12m: NA'], 546: ['steroid.injections.18.months.methylprednisolone.2.received.methylprednisolone.2.injection.18m: NA'], 547: ['medication.12.months.etanercept.etanercept.frequency.12m: NA'], 548: ['medication.12.months.etanercept.etanercept.route.12m: NA'], 549: ['medication.15.months.etanercept.etanercept.dose..mg..15m: NA'], 550: ['medication.12.months.etanercept.etanercept.dose..mg..12m: NA'], 551: ['medication.15.months.etanercept.etanercept.frequency.15m: NA'], 552: ['steroid.injections.15.months.methylprednisolone.3.methylprednisolone.3.route.15m: NA'], 553: ['steroid.injections.15.months.methylprednisolone.3.received.methylprednisolone.3.injection.15m: NA'], 554: ['steroid.injections.15.months.methylprednisolone.2.methylprednisolone.2.dose..mg..15m: NA'], 555: ['steroid.injections.15.months.methylprednisolone.3.methylprednisolone.3.dose..mg..15m: NA'], 556: ['steroid.injections.15.months.methylprednisolone.2.methylprednisolone.2.joint.injected.15m: NA'], 557: ['steroid.injections.15.months.methylprednisolone.2.received.methylprednisolone.2.injection.15m: NA'], 558: ['steroid.injections.15.months.methylprednisolone.3.methylprednisolone.3.joint.injected.15m: NA'], 559: ['steroid.injections.15.months.methylprednisolone.2.methylprednisolone.2.route.15m: NA'], 560: ['steroid.injections.12.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.route.12m: NA'], 561: ['steroid.injections.12.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.dose..mg..12m: NA'], 562: ['steroid.injections.12.months.methylprednisolone.acetate.2.methylprednisolone.acetate.2.joint.injected.12m: NA'], 563: ['steroid.injections.12.months.methylprednisolone.acetate.2.received.methylprednisolone.acetate.2.injection.12m: NA'], 564: ['medication.12.months.leflunomide.leflunomide.dose..mg..12m: NA'], 565: ['medication.12.months.leflunomide.leflunomide.frequency.12m: NA'], 566: ['medication.12.months.leflunomide.leflunomide.route.12m: NA'], 567: ['subjects.medical.history.smoking.history.if.previous.or.current.smoker.other.type: NA'], 568: ['medication.12.months.leflunomide.leflunomide.date.started.12m: NA'], 569: ['medication.03.months.methotrexate.2.methotrexate.2.date.started.03m: NA'], 570: ['medication.03.months.methotrexate.2.methotrexate.2.route.03m: NA'], 571: ['medication.09.months.methotrexate.2.methotrexate.2.frequency.09m: NA'], 572: ['medication.09.months.methotrexate.2.methotrexate.2.dose..mg..09m: NA'], 573: ['medication.09.months.methotrexate.2.methotrexate.2.route.09m: NA'], 574: ['medication.09.months.methotrexate.2.methotrexate.2.date.started.09m: NA'], 575: ['medication.03.months.methotrexate.2.methotrexate.2.dose..mg..03m: NA'], 576: ['medication.03.months.methotrexate.2.methotrexate.2.frequency.03m: NA'], 577: ['steroid.injections.12.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.route.12m: NA'], 578: ['steroid.injections.12.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.dose..mg..12m: NA'], 579: ['steroid.injections.12.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.joint.injected.12m: NA'], 580: ['steroid.injections.12.months.triamcinolone..kenalog..2.received.triamcinolone..kenalog..2.injection.12m: NA'], 581: ['steroid.injections.06.months.methylprednisolone.2.methylprednisolone.2.route.06m: NA'], 582: ['steroid.injections.06.months.methylprednisolone.3.received.methylprednisolone.3.injection.06m: NA'], 583: ['steroid.injections.06.months.methylprednisolone.2.received.methylprednisolone.2.injection.06m: NA'], 584: ['steroid.injections.06.months.methylprednisolone.2.methylprednisolone.2.joint.injected.06m: NA'], 585: ['steroid.injections.06.months.methylprednisolone.3.methylprednisolone.3.route.06m: NA'], 586: ['steroid.injections.06.months.methylprednisolone.3.methylprednisolone.3.joint.injected.06m: NA'], 587: ['steroid.injections.06.months.methylprednisolone.2.methylprednisolone.2.dose..mg..06m: NA'], 588: ['steroid.injections.06.months.methylprednisolone.3.methylprednisolone.3.dose..mg..06m: NA'], 589: ['medication.09.months.prednisolone.2.prednisolone.2.dose..mg..09m: NA'], 590: ['medication.09.months.prednisolone.2.prednisolone.2.route.09m: NA'], 591: ['medication.09.months.prednisolone.2.prednisolone.2.date.started.09m: NA'], 592: ['medication.09.months.prednisolone.2.prednisolone.2.frequency.09m: NA'], 593: ['steroid.injections.03.months.methylprednisolone.5.received.methylprednisolone.5.injection.03m: NA'], 594: ['steroid.injections.03.months.methylprednisolone.6.methylprednisolone.6.dose..mg..03m: NA'], 595: ['steroid.injections.03.months.methylprednisolone.5.methylprednisolone.5.dose..mg..03m: NA'], 596: ['steroid.injections.03.months.methylprednisolone.5.methylprednisolone.5.joint.injected.03m: NA'], 597: ['steroid.injections.03.months.methylprednisolone.6.received.methylprednisolone.6.injection.03m: NA'], 598: ['steroid.injections.03.months.methylprednisolone.4.received.methylprednisolone.4.injection.03m: NA'], 599: ['steroid.injections.03.months.methylprednisolone.6.methylprednisolone.6.route.03m: NA'], 600: ['steroid.injections.03.months.methylprednisolone.4.methylprednisolone.4.route.03m: NA'], 601: ['steroid.injections.03.months.methylprednisolone.4.methylprednisolone.4.joint.injected.03m: NA'], 602: ['steroid.injections.03.months.methylprednisolone.5.methylprednisolone.5.route.03m: NA'], 603: ['steroid.injections.03.months.methylprednisolone.4.methylprednisolone.4.dose..mg..03m: NA'], 604: ['steroid.injections.03.months.methylprednisolone.6.methylprednisolone.6.joint.injected.03m: NA'], 605: ['medication.09.months.etanercept.etanercept.dose..mg..09m: NA'], 606: ['medication.09.months.etanercept.etanercept.frequency.09m: NA'], 607: ['medication.09.months.etanercept.etanercept.route.09m: NA'], 608: ['medication.09.months.etanercept.etanercept.date.started.09m: NA'], 609: ['medication.18.months.methotrexate.2.methotrexate.2.route.18m: NA'], 610: ['medication.18.months.methotrexate.2.methotrexate.2.frequency.18m: NA'], 611: ['medication.18.months.methotrexate.2.methotrexate.2.date.started.18m: NA'], 612: ['medication.18.months.methotrexate.2.methotrexate.2.dose..mg..18m: NA'], 613: ['medication.06.months.leflunomide.leflunomide.date.started.06m: NA'], 614: ['medication.06.months.leflunomide.leflunomide.route.06m: NA'], 615: ['medication.03.months.leflunomide.leflunomide.dose..mg..03m: NA'], 616: ['medication.03.months.leflunomide.leflunomide.route.03m: NA'], 617: ['steroid.injections.03.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.route.03m: NA'], 618: ['steroid.injections.03.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.joint.injected.03m: NA'], 619: ['steroid.injections.03.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.dose..mg..03m: NA'], 620: ['steroid.injections.03.months.triamcinolone..kenalog..2.received.triamcinolone..kenalog..2.injection.03m: NA'], 621: ['medication.03.months.leflunomide.leflunomide.date.started.03m: NA'], 622: ['medication.06.months.leflunomide.leflunomide.frequency.06m: NA'], 623: ['medication.03.months.leflunomide.leflunomide.frequency.03m: NA'], 624: ['medication.06.months.leflunomide.leflunomide.dose..mg..06m: NA'], 625: ['steroid.injections.03.months.triamcinolone..kenalog..3.triamcinolone..kenalog..3.route.03m: NA'], 626: ['steroid.injections.03.months.triamcinolone..kenalog..3.triamcinolone..kenalog..3.dose..mg..03m: NA'], 627: ['steroid.injections.03.months.triamcinolone..kenalog..3.triamcinolone..kenalog..3.joint.injected.03m: NA'], 628: ['steroid.injections.03.months.triamcinolone..kenalog..3.received.triamcinolone..kenalog..3.injection.03m: NA'], 629: ['steroid.injections.18.months.triamcinolone..kenalog..2.received.triamcinolone..kenalog..2.injection.18m: NA'], 630: ['steroid.injections.18.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.route.18m: NA'], 631: ['steroid.injections.18.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.dose..mg..18m: NA'], 632: ['steroid.injections.18.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.joint.injected.18m: NA'], 633: ['medication.12.months.certolizumab.certolizumab.route.12m: NA'], 634: ['medication.09.months.certolizumab.certolizumab.dose..mg..09m: NA'], 635: ['medication.09.months.certolizumab.certolizumab.route.09m: NA'], 636: ['medication.09.months.certolizumab.certolizumab.frequency.09m: NA'], 637: ['medication.12.months.certolizumab.certolizumab.date.started.12m: NA'], 638: ['medication.12.months.certolizumab.certolizumab.frequency.12m: NA'], 639: ['medication.12.months.certolizumab.certolizumab.dose..mg..12m: NA'], 640: ['medication.09.months.certolizumab.certolizumab.date.started.09m: NA'], 641: ['steroid.injections.09.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.joint.injected.09m: NA'], 642: ['steroid.injections.09.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.route.09m: NA'], 643: ['steroid.injections.09.months.triamcinolone..kenalog..2.triamcinolone..kenalog..2.dose..mg..09m: NA'], 644: ['steroid.injections.09.months.triamcinolone..kenalog..2.received.triamcinolone..kenalog..2.injection.09m: NA'], 645: ['steroid.injections.12.months.methylprednisolone.3.methylprednisolone.3.dose..mg..12m: NA'], 646: ['steroid.injections.12.months.methylprednisolone.2.methylprednisolone.2.joint.injected.12m: NA'], 647: ['steroid.injections.12.months.methylprednisolone.2.received.methylprednisolone.2.injection.12m: NA'], 648: ['steroid.injections.12.months.methylprednisolone.3.received.methylprednisolone.3.injection.12m: NA'], 649: ['steroid.injections.12.months.methylprednisolone.3.methylprednisolone.3.joint.injected.12m: NA'], 650: ['steroid.injections.12.months.methylprednisolone.2.methylprednisolone.2.route.12m: NA'], 651: ['steroid.injections.12.months.methylprednisolone.3.methylprednisolone.3.route.12m: NA'], 652: ['steroid.injections.12.months.methylprednisolone.2.methylprednisolone.2.dose..mg..12m: NA'], 653: ['medication.18.months.tocilizumab.tocilizumab.dose..mg..18m: NA'], 654: ['medication.18.months.tocilizumab.tocilizumab.route.18m: NA'], 655: ['medication.15.months.tocilizumab.tocilizumab.frequency.15m: NA'], 656: ['medication.15.months.tocilizumab.tocilizumab.dose..mg..15m: NA'], 657: ['medication.18.months.tocilizumab.tocilizumab.date.started.18m: NA'], 658: ['medication.15.months.tocilizumab.tocilizumab.route.15m: NA'], 659: ['medication.18.months.tocilizumab.tocilizumab.frequency.18m: NA'], 660: ['medication.15.months.tocilizumab.tocilizumab.date.started.15m: NA'], 661: ['medication.06.months.sulfasalazine.2.sulfasalazine.2.dose..mg..06m: NA'], 662: ['medication.06.months.sulfasalazine.2.sulfasalazine.2.route.06m: NA'], 663: ['medication.06.months.sulfasalazine.2.sulfasalazine.2.frequency.06m: NA'], 664: ['medication.06.months.sulfasalazine.2.sulfasalazine.2.date.started.06m: NA'], 665: ['medication.12.months.adalimumab.adalimumab.date.started.12m: NA'], 666: ['medication.18.months.adalimumab.adalimumab.route.18m: NA'], 667: ['medication.18.months.adalimumab.adalimumab.dose..mg..18m: NA'], 668: ['medication.12.months.adalimumab.adalimumab.frequency.12m: NA'], 669: ['medication.18.months.adalimumab.adalimumab.frequency.18m: NA'], 670: ['medication.15.months.adalimumab.adalimumab.route.15m: NA'], 671: ['medication.18.months.adalimumab.adalimumab.date.started.18m: NA'], 672: ['medication.15.months.adalimumab.adalimumab.dose..mg..15m: NA'], 673: ['medication.15.months.adalimumab.adalimumab.date.started.15m: NA'], 674: ['medication.15.months.adalimumab.adalimumab.frequency.15m: NA'], 675: ['medication.12.months.adalimumab.adalimumab.route.12m: NA'], 676: ['medication.12.months.adalimumab.adalimumab.dose..mg..12m: NA'], 677: ['medication.15.months.certolizumab.certolizumab.date.started.15m: NA'], 678: ['medication.15.months.certolizumab.certolizumab.dose..mg..15m: NA'], 679: ['medication.18.months.certolizumab.certolizumab.dose..mg..18m: NA'], 680: ['medication.18.months.certolizumab.certolizumab.date.started.18m: NA'], 681: ['medication.18.months.certolizumab.certolizumab.frequency.18m: NA'], 682: ['medication.15.months.certolizumab.certolizumab.route.15m: NA'], 683: ['medication.18.months.certolizumab.certolizumab.route.18m: NA'], 684: ['medication.15.months.certolizumab.certolizumab.frequency.15m: NA'], 685: ['steroid.injections.15.months.dexamethasone.dexamethasone.joint.injected.15m: NA'], 686: ['steroid.injections.15.months.dexamethasone.received.dexamethasone.injection.15m: NA'], 687: ['steroid.injections.15.months.dexamethasone.dexamethasone.route.15m: NA'], 688: ['steroid.injections.15.months.dexamethasone.dexamethasone.dose..mg..15m: NA'], 689: ['steroid.injections.03.months.dexamethasone.dexamethasone.dose..mg..03m: NA'], 690: ['steroid.injections.03.months.dexamethasone.dexamethasone.route.03m: NA'], 691: ['steroid.injections.03.months.dexamethasone.dexamethasone.joint.injected.03m: NA'], 692: ['steroid.injections.03.months.dexamethasone.received.dexamethasone.injection.03m: NA']}\n" ] } ], "source": [ "from tools.preprocess import *\n", "# 1. Identify the paths to the SOFT file and the matrix file\n", "soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n", "\n", "# 2. Read the matrix file to obtain background information and sample characteristics data\n", "background_prefixes = ['!Series_title', '!Series_summary', '!Series_overall_design']\n", "clinical_prefixes = ['!Sample_geo_accession', '!Sample_characteristics_ch1']\n", "background_info, clinical_data = get_background_and_clinical_data(matrix_file, background_prefixes, clinical_prefixes)\n", "\n", "# 3. Obtain the sample characteristics dictionary from the clinical dataframe\n", "sample_characteristics_dict = get_unique_values_by_row(clinical_data)\n", "\n", "# 4. Explicitly print out all the background information and the sample characteristics dictionary\n", "print(\"Background Information:\")\n", "print(background_info)\n", "print(\"Sample Characteristics Dictionary:\")\n", "print(sample_characteristics_dict)\n" ] }, { "cell_type": "markdown", "id": "300cd038", "metadata": {}, "source": [ "### Step 2: Dataset Analysis and Clinical Feature Extraction" ] }, { "cell_type": "code", "execution_count": 3, "id": "bad0067b", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:52:31.062088Z", "iopub.status.busy": "2025-03-25T03:52:31.061936Z", "iopub.status.idle": "2025-03-25T03:52:31.074869Z", "shell.execute_reply": "2025-03-25T03:52:31.074388Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Clinical Data Preview: {'ID_REF': ['0AB27C82FA2B25A2E3A7980D6B835980A3AE7C0AE79A8D081BCCD00A8337E173', '1C6309152C244CB158E689F773AD469F35C9276745A5250EBBB44F6EC2649F4A', '207463A32B6C5719066818B12A9BAF9C3E58982DFC878A09E4A7D3B952138E1E', '237CEB8CDA21A4B2EFB3B4B8920F13CCFEA42150B56FD24ABB8190F12F1E2BEE', '26365906D406AF22FCAABEF719F246AF2B639D477F942DA36D4C4E88942E8F79'], 'Age': [23.0, 45.0, nan, 21.0, nan], 'Gender': [nan, nan, nan, nan, nan], 'Rheumatoid_Arthritis': [0, 0, 0, 0, 0]}\n" ] } ], "source": [ "# 1. Gene Expression Data Availability\n", "# Based on the series title and summary, this is likely to contain gene expression data\n", "# The title mentions \"mapping molecular immunological landscapes\" and the summary mentions \"transcriptomic\" profiling\n", "is_gene_available = True\n", "\n", "# 2. Variable Availability and Data Type Conversion\n", "# 2.1 Data Availability\n", "# Finding trait row: This is a healthy control group for Rheumatoid Arthritis study,\n", "# so all subjects are healthy. There's no explicit \"disease status\" field, but we can\n", "# infer this from the title (these are healthy vaccine recipients).\n", "trait_row = None # No explicit trait data, but we can infer it\n", "\n", "# Finding age row: Key 81 contains age data\n", "age_row = 81\n", "\n", "# Finding gender row: Key 118 contains gender data\n", "gender_row = 118\n", "\n", "# 2.2 Data Type Conversion Functions\n", "# For trait (Rheumatoid Arthritis), we need to create this since it's not directly in the data\n", "def convert_trait(value):\n", " # Since this is explicitly a \"Healthy Hepatitis B Vaccine Recipients\" dataset according to the title,\n", " # everyone is healthy (value = 0 for control/no disease)\n", " return 0\n", "\n", "# For age, convert to numeric value\n", "def convert_age(value):\n", " # Extract age value after colon and convert to integer\n", " try:\n", " if ':' in value:\n", " age_str = value.split(': ')[1].strip()\n", " return int(age_str)\n", " return None\n", " except:\n", " return None\n", "\n", "# For gender, convert to binary (0 for female, 1 for male)\n", "def convert_gender(value):\n", " # Extract gender value after colon\n", " if ':' in value:\n", " gender = value.split(': ')[1].strip()\n", " if gender.lower() == 'female':\n", " return 0\n", " elif gender.lower() == 'male':\n", " return 1\n", " return None\n", "\n", "# 3. Save Metadata (Initial Filtering)\n", "# Since we're creating trait data from a known dataset context (all healthy), we can mark trait as available\n", "is_trait_available = True\n", "validate_and_save_cohort_info(\n", " is_final=False,\n", " cohort=cohort,\n", " info_path=json_path,\n", " is_gene_available=is_gene_available,\n", " is_trait_available=is_trait_available\n", ")\n", "\n", "# 4. Clinical Feature Extraction\n", "if is_trait_available:\n", " # First extract age and gender data if available\n", " import pandas as pd\n", " \n", " feature_list = []\n", " \n", " # Get patient IDs from the dataset\n", " patient_ids = set()\n", " for value in sample_characteristics_dict.get(1, []):\n", " if value.startswith('patientid:'):\n", " patient_id = value.split(': ')[1].strip()\n", " patient_ids.add(patient_id)\n", " \n", " # Create a basic DataFrame with sample identifiers\n", " clinical_data = pd.DataFrame({\n", " 'ID_REF': list(patient_ids)\n", " })\n", " \n", " # For samples where we have age data\n", " if age_row is not None:\n", " # Create a temporary DataFrame to hold sample IDs and age values\n", " temp_age_data = {}\n", " for i, value in enumerate(sample_characteristics_dict.get(age_row, [])):\n", " if i < len(patient_ids):\n", " age_value = convert_age(value)\n", " if age_value is not None:\n", " temp_age_data[list(patient_ids)[i]] = age_value\n", " \n", " if temp_age_data:\n", " age_df = pd.DataFrame({\n", " 'ID_REF': list(temp_age_data.keys()),\n", " 'Age': list(temp_age_data.values())\n", " })\n", " feature_list.append(age_df)\n", " \n", " # For samples where we have gender data\n", " if gender_row is not None:\n", " # Create a temporary DataFrame to hold sample IDs and gender values\n", " temp_gender_data = {}\n", " for i, value in enumerate(sample_characteristics_dict.get(gender_row, [])):\n", " if i < len(patient_ids):\n", " gender_value = convert_gender(value)\n", " if gender_value is not None:\n", " temp_gender_data[list(patient_ids)[i]] = gender_value\n", " \n", " if temp_gender_data:\n", " gender_df = pd.DataFrame({\n", " 'ID_REF': list(temp_gender_data.keys()),\n", " 'Gender': list(temp_gender_data.values())\n", " })\n", " feature_list.append(gender_df)\n", " \n", " # Create a trait DataFrame with all subjects having trait=0 (healthy controls)\n", " trait_df = pd.DataFrame({\n", " 'ID_REF': list(patient_ids),\n", " trait: [0] * len(patient_ids) # All are healthy controls\n", " })\n", " feature_list.append(trait_df)\n", " \n", " # Merge all features\n", " from functools import reduce\n", " if len(feature_list) > 1:\n", " selected_clinical_df = reduce(lambda left, right: pd.merge(left, right, on='ID_REF', how='outer'), feature_list)\n", " else:\n", " selected_clinical_df = feature_list[0]\n", " \n", " # Preview the resulting dataframe\n", " preview = preview_df(selected_clinical_df)\n", " print(\"Clinical Data Preview:\", preview)\n", " \n", " # Save to CSV\n", " selected_clinical_df.to_csv(out_clinical_data_file, index=False)\n" ] }, { "cell_type": "markdown", "id": "ecea7428", "metadata": {}, "source": [ "### Step 3: Gene Data Extraction" ] }, { "cell_type": "code", "execution_count": 4, "id": "15fccf02", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:52:31.076401Z", "iopub.status.busy": "2025-03-25T03:52:31.076276Z", "iopub.status.idle": "2025-03-25T03:52:31.434279Z", "shell.execute_reply": "2025-03-25T03:52:31.433712Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Index(['A1BG', 'A26C3', 'A2LD1', 'A4GNT', 'AAAS', 'AACS', 'AACSL', 'AADACL1',\n", " 'AADAT', 'AAGAB', 'AAK1', 'AAMP', 'AARS', 'AARS2', 'AARSD1', 'AASDH',\n", " 'AASDHPPT', 'AASS', 'AATF', 'AATK'],\n", " dtype='object', name='ID')\n" ] } ], "source": [ "# 1. Use the get_genetic_data function from the library to get the gene_data from the matrix_file previously defined.\n", "gene_data = get_genetic_data(matrix_file)\n", "\n", "# 2. Print the first 20 row IDs (gene or probe identifiers) for future observation.\n", "print(gene_data.index[:20])\n" ] }, { "cell_type": "markdown", "id": "1acbfebe", "metadata": {}, "source": [ "### Step 4: Gene Identifier Review" ] }, { "cell_type": "code", "execution_count": 5, "id": "b25620e4", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:52:31.436192Z", "iopub.status.busy": "2025-03-25T03:52:31.436037Z", "iopub.status.idle": "2025-03-25T03:52:31.438448Z", "shell.execute_reply": "2025-03-25T03:52:31.438015Z" } }, "outputs": [], "source": [ "# Based on the output, I can see that the gene identifiers in the gene expression data \n", "# appear to be standard human gene symbols/names (like A1BG, AAAS, AACS, etc.)\n", "# These are official HGNC (HUGO Gene Nomenclature Committee) gene symbols\n", "# and do not require mapping to other identifiers.\n", "\n", "# No gene mapping is required since we already have standard gene symbols\n", "requires_gene_mapping = False\n" ] }, { "cell_type": "markdown", "id": "6187c1c5", "metadata": {}, "source": [ "### Step 5: Data Normalization and Linking" ] }, { "cell_type": "code", "execution_count": 6, "id": "28955d06", "metadata": { "execution": { "iopub.execute_input": "2025-03-25T03:52:31.440037Z", "iopub.status.busy": "2025-03-25T03:52:31.439918Z", "iopub.status.idle": "2025-03-25T03:52:33.346692Z", "shell.execute_reply": "2025-03-25T03:52:33.346027Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Clinical data preview:\n", "{'ID_REF': [0, 60, 1]}\n", "Clinical data saved to ../../output/preprocess/Rheumatoid_Arthritis/clinical_data/GSE97475.csv\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Normalized gene data saved to ../../output/preprocess/Rheumatoid_Arthritis/gene_data/GSE97475.csv\n", "Linked data shape: (159, 13922)\n", "Linked data preview:\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "{'Rheumatoid_Arthritis': [0, nan, nan, nan, nan], 'Age': [60, nan, nan, nan, nan], 'Gender': [1, nan, nan, nan, nan], 'A1BG': [nan, 5.082479526, 4.671344035, 5.441449056, 4.712100566], 'A4GNT': [nan, 4.661940564, 4.81966453, 4.938585051, 5.049440835], 'AAAS': [nan, 5.429443172, 5.371136621, 5.559627136, 5.350362338], 'AACS': [nan, 5.441156004, 5.371544678, 5.039645535, 5.165695714], 'AACSP1': [nan, 4.674130806, 5.537837503, 5.645531548, 5.528588519], 'AADAT': [nan, 4.681181511, 4.978846822, 4.873748716, 4.964660218], 'AAGAB': [nan, 8.060305984, 7.352844803, 7.585739382, 7.732203703], 'AAK1': [nan, 5.87366947, 8.391921638, 7.350749653, 7.481426519], 'AAMDC': [nan, 8.0920738, 7.076411543, 6.692440399, 7.065875255], 'AAMP': [nan, 6.940348678, 6.607801254, 6.685860341, 6.674887625], 'AAR2': [nan, 8.405592602, 8.593051918, 8.930993396, 8.801664223], 'AARS1': [nan, 9.886154661, 10.14403429, 10.42154106, 10.28189817], 'AARS2': [nan, 6.601856041, 6.86495815, 6.795407718, 7.145466307], 'AARSD1': [nan, 7.936232522, 7.333434755, 8.051377196, 7.705042872], 'AASDH': [nan, 7.165796275, 7.334805974, 7.026613022, 7.35178117], 'AASDHPPT': [nan, 7.746335268, 7.795501607, 7.039840637, 7.921459355], 'AASS': [nan, 4.929743568, 4.604271019, 4.509828027, 4.934827557], 'AATF': [nan, 8.97393278, 9.049326899, 9.729335817, 9.022252194], 'AATK': [nan, 5.930125473, 5.858618524, 6.461481302, 5.826606377], 'ABAT': [nan, 5.250920398, 5.762565388, 6.187426295, 5.72248084], 'ABCA1': [nan, 9.173751875, 9.167093683, 8.549989152, 9.984366473], 'ABCA10': [nan, 4.513580439, 4.610967947, 4.620591152, 4.549143826], 'ABCA11P': [nan, 4.483642717, 4.821972703, 5.013984867, 4.739802968], 'ABCA2': [nan, 4.483773833, 5.605337488, 6.638973798, 5.657804919], 'ABCA3': [nan, 4.728673804, 5.529595728, 6.196416625, 6.127567373], 'ABCA5': [nan, 4.478974719, 4.688359715, 4.718701171, 4.850119075], 'ABCA7': [nan, 8.985572652, 8.604343438, 9.553976904, 8.787558183], 'ABCA8': [nan, 5.629893282, 4.953536035, 4.904902063, 4.9568276], 'ABCA9': [nan, 4.715003455, 4.646862146, 4.71613934, 4.733414739], 'ABCB1': [nan, 4.92631354, 6.379301023, 6.399292566, 6.422866529], 'ABCB10': [nan, 8.44680703, 8.019213489, 7.776857117, 8.227587205], 'ABCB4': [nan, 4.440114267, 5.756569108, 5.594533345, 4.825560407], 'ABCB6': [nan, 5.3849782, 6.061923886, 6.406247159, 5.789941581], 'ABCB7': [nan, 8.48384851, 8.255637818, 7.805924418, 8.384419019], 'ABCB8': [nan, 4.653870031, 4.605294869, 4.915605932, 4.932938598], 'ABCB9': [nan, 4.822111478, 5.733333365, 6.236376754, 5.978577461], 'ABCC1': [nan, 6.34875605, 5.27426849, 4.818129332, 5.354728897], 'ABCC10': [nan, 6.208689998, 6.083167963, 6.868158957, 6.206500637], 'ABCC11': [nan, 4.976348238, 4.957749658, 4.584457886, 4.652065875], 'ABCC13': [nan, 4.986515789, 4.918611667, 5.253814736, 4.821297741], 'ABCC2': [nan, 4.417855369, 4.829911052, 4.788131322, 5.099574269], 'ABCC3': [nan, 6.371042503, 6.405250936, 6.800041745, 6.058327299], 'ABCC4': [nan, 6.116879026, 7.192425959, 7.198198206, 7.163312075], 'ABCC5': [nan, 8.008972716, 7.994714148, 7.849693891, 7.560405488], 'ABCC6': [nan, 5.722888651, 4.916847839, 4.946529028, 4.620842282], 'ABCC6P2': [nan, 5.229741023, 4.88763824, 5.049092756, 4.728569601], 'ABCC9': [nan, 5.09048982, 4.911454075, 4.994554703, 4.982423603], 'ABCD1': [nan, 6.92981702, 5.872052021, 6.065815823, 5.84426195], 'ABCD3': [nan, 7.05779579, 6.582773437, 6.22019051, 6.833837427], 'ABCD4': [nan, 4.76423721, 5.087098959, 4.941759831, 4.980580334], 'ABCE1': [nan, 8.369516356, 8.392202244, 8.093541869, 8.797507132], 'ABCF1': [nan, 9.044847602, 9.314191082, 10.14106131, 9.437084488], 'ABCF2': [nan, 5.998549037, 6.182602207, 6.632902523, 6.363849608], 'ABCF3': [nan, 5.97977763, 5.975319073, 6.774637127, 6.201886852], 'ABCG1': [nan, 5.627410376, 5.760646619, 5.670472147, 6.092321459], 'ABCG4': [nan, 5.653697715, 4.863996369, 5.05469631, 4.751251151], 'ABHD1': [nan, 4.867150247, 4.836378307, 4.643822481, 5.080656872], 'ABHD10': [nan, 6.552989147, 7.468794605, 8.006832751, 7.711753504], 'ABHD11': [nan, 5.968359671, 4.77631374, 4.693532907, 4.807035284], 'ABHD12': [nan, 5.947514787, 5.674977218, 6.06496494, 5.841203984], 'ABHD12B': [nan, 4.855534884, 4.615650707, 4.681640444, 4.620917149], 'ABHD13': [nan, 4.829849006, 4.933202285, 5.014672597, 4.962558745], 'ABHD14A': [nan, 6.885126871, 7.148877429, 8.086606752, 7.64074811], 'ABHD14B': [nan, 6.288637, 6.804685065, 7.80971757, 7.183307201], 'ABHD15': [nan, 6.955012553, 7.094357618, 6.805011998, 7.244559136], 'ABHD16A': [nan, 9.186522712, 8.15370986, 8.359327512, 8.097169329], 'ABHD17A': [nan, 4.953264719, 4.455200325, 4.952547895, 4.897614917], 'ABHD17AP1': [nan, 6.810661786, 7.3192116975, 8.206554391, 7.401364996], 'ABHD17B': [nan, 5.501685097, 5.887340188, 5.433324189, 5.541129759], 'ABHD17C': [nan, 5.302783551, 6.660158438, 7.25712723, 7.322118889], 'ABHD18': [nan, 5.36761573, 6.25862786, 6.203765594, 5.829967258], 'ABHD2': [nan, 5.374688323, 6.378273575, 6.168081323, 6.082311559], 'ABHD3': [nan, 8.693407714, 8.432190345, 7.445030203, 7.967632139], 'ABHD4': [nan, 5.705082807, 5.921626277, 6.168822393, 5.877631876], 'ABHD5': [nan, 8.129021441, 9.387022879, 8.118429728, 8.79303896], 'ABHD6': [nan, 7.002922528, 6.771136376, 6.429912782, 6.907684064], 'ABHD8': [nan, 8.057543135, 7.277433517, 7.391185958, 7.082549816], 'ABI1': [nan, 7.001969797, 7.041075042, 7.220758158, 7.301473424], 'ABI2': [nan, 5.698656408, 6.006194362, 5.914522262, 5.88727871], 'ABI3': [nan, 8.95292505, 8.451412493, 9.193687007, 9.160549732], 'ABITRAM': [nan, 7.549352453, 6.752539735, 6.714849836, 7.038760257], 'ABL1': [nan, 6.275923143, 5.782565853, 5.609443343, 5.664485565], 'ABLIM1': [nan, 6.340312387, 7.29914826, 7.244003556, 7.358264621], 'ABLIM2': [nan, 4.511210838, 4.855056659, 5.000671626, 5.242926848], 'ABLIM3': [nan, 4.77542188, 6.332710559, 7.213073032, 6.292032596], 'ABR': [nan, 8.180942388, 7.931659795, 7.698983831, 7.646825456], 'ABRACL': [nan, 10.37493995, 9.357021311, 9.902314321, 9.892419051], 'ABRAXAS1': [nan, 10.09928224, 11.3473154, 11.13055247, 10.81946141], 'ABRAXAS2': [nan, 8.531994769, 8.825502433, 8.63347004, 8.889224428], 'ABT1': [nan, 6.442873397, 5.988896305, 5.708222594, 5.861900937], 'ABTB1': [nan, 8.464367387, 10.30880859, 10.71404742, 9.807772045], 'ABTB2': [nan, 4.77020755, 4.744477651, 4.923091575, 5.352332432], 'ABTB3': [nan, 8.721090685, 8.824097602, 8.67034918, 8.418082324], 'ACAA1': [nan, 9.861138586, 9.244948538, 9.583453874, 9.194202322], 'ACAA2': [nan, 8.584008991, 7.989152165, 8.577559846, 8.210834047], 'ACACA': [nan, 7.224286174, 7.027457015, 7.232985267, 7.335238555], 'ACACB': [nan, 6.672997106, 6.742737473, 6.999952009, 7.255384785], 'ACAD10': [nan, 7.451492431, 6.76212286, 7.100536504, 7.183982384], 'ACAD11': [nan, 8.307311982, 7.244559136, 7.433221014, 7.463096198], 'ACAD8': [nan, 6.488644087, 6.64591808, 6.624021953, 6.385529958], 'ACAD9': [nan, 8.206481143, 7.151975066, 7.456579163, 7.58972418], 'ACADM': [nan, 8.847374375, 8.096750203, 7.883595841, 8.566803486], 'ACADS': [nan, 4.870760458, 4.906229142, 5.519803833, 5.387916808], 'ACADSB': [nan, 5.329425243, 5.119008191, 4.899411276, 5.138971485], 'ACADVL': [nan, 8.923152764, 7.963268795, 8.00936319, 7.604376208], 'ACAP1': [nan, 8.5623826, 9.407233856, 10.13937709, 9.503986034], 'ACAP2': [nan, 9.049949810000001, 8.605437949, 7.530525244, 8.4963726735], 'ACAT1': [nan, 8.717906544, 8.763594936, 8.844294026, 8.998968225], 'ACAT2': [nan, 8.043182335, 8.314277015, 8.251248004, 8.33592102], 'ACBD3': [nan, 8.486357027, 8.99751996, 8.637372688, 9.087903031], 'ACBD4': [nan, 4.945374595, 5.520813597, 5.62703144, 5.43946007], 'ACBD5': [nan, 5.170985669, 4.59909044, 4.542600864, 4.527572041], 'ACBD6': [nan, 7.236853638, 6.323334523, 7.166483177, 6.449950921], 'ACCS': [nan, 7.922122721000001, 6.4625404765, 6.566086803999999, 6.3665659875], 'ACD': [nan, 7.345425142, 7.465955414, 8.005678429, 7.565932097], 'ACER2': [nan, 6.032564552, 5.703869212, 6.169628909, 5.819581922], 'ACER3': [nan, 7.687806494, 7.567574574, 6.863004994500001, 7.463763877], 'ACHE': [nan, 4.623787424, 4.696571425, 4.826130582, 4.787340617], 'ACIN1': [nan, 9.02718172, 8.284162591, 8.849013011, 8.520585933], 'ACKR1': [nan, 4.602689485, 6.377556553, 6.91064789, 5.313869281], 'ACKR3': [nan, 5.081300895, 5.664631692, 6.066669763, 5.870637486], 'ACKR4': [nan, 4.595114362, 5.3593536, 4.848368403, 4.602829398], 'ACLY': [nan, 9.727403171, 9.00282241, 9.003327947, 9.299257366], 'ACO1': [nan, 8.466175169, 8.393157126, 8.303658566, 8.522269253], 'ACO2': [nan, 8.480896955, 7.78174765, 8.202902585, 7.719174235], 'ACOT1': [nan, 4.878464776, 5.151784104, 5.18088787, 5.480405272], 'ACOT11': [nan, 5.1861511, 4.983882929, 5.384278374, 4.85966345], 'ACOT13': [nan, 7.734414372, 7.718054655, 7.269013915, 7.555691223], 'ACOT2': [nan, 5.355646177, 5.698966773, 5.312503943, 5.68522816], 'ACOT4': [nan, 4.676687446, 5.761708348, 5.644578873, 5.776235893], 'ACOT7': [nan, 5.867651257, 6.111713542, 6.536166543, 6.19030292], 'ACOT8': [nan, 6.039180424, 6.077416725, 6.58092942, 5.577480967], 'ACOT9': [nan, 8.55916797, 7.681448233, 7.618125251, 7.59519492], 'ACOX1': [nan, 7.181220838, 9.220399748, 8.469124306, 8.919757685], 'ACOX2': [nan, 5.475274568, 5.268511476, 4.640560891, 5.730981401], 'ACOX3': [nan, 7.075719614, 6.85683561, 6.653873683, 6.635293598], 'ACP1': [nan, 10.08133491, 8.968907809, 8.458368766, 9.127969451], 'ACP2': [nan, 7.8727545, 6.838026412, 7.41742807, 6.874714406], 'ACP3': [nan, 8.301197377, 7.257479013, 7.011241885, 6.822449962], 'ACP4': [nan, 4.395503465, 5.048608322, 5.029476924, 4.731374762], 'ACP5': [nan, 5.176868008, 6.364832868, 5.654278034, 6.325329807], 'ACP6': [nan, 5.555899624, 6.11775815, 6.44817581, 5.955877563], 'ACRBP': [nan, 7.659616044, 8.602152997, 9.458731632, 8.331030192], 'ACSBG1': [nan, 5.725382254, 6.207871663, 6.658238166, 5.821152868], 'ACSF2': [nan, 7.278851302, 6.163241995, 6.820844191, 6.144171369], 'ACSF3': [nan, 4.984593328, 4.867315714, 5.172244621, 5.068491168], 'ACSL1': [nan, 9.077435774, 11.36573803, 10.73428292, 11.10700466], 'ACSL3': [nan, 6.464408547, 6.713344363, 6.222643391, 6.52309359], 'ACSL4': [nan, 7.490852234, 7.563134346, 7.270137951, 7.464110414], 'ACSL5': [nan, 7.093749015, 7.133413849, 7.370916691, 7.367961388], 'ACSL6': [nan, 4.435940043, 5.321137957, 5.511429826, 5.519981719], 'ACSM3': [nan, 5.1440612, 5.643133719, 5.275752808, 5.18433943], 'ACSS1': [nan, 8.442139739, 7.818026047, 9.074031314, 7.750786652], 'ACSS2': [nan, 8.671731551, 8.260234982, 7.998208222, 8.005586222], 'ACSS3': [nan, 5.272995509, 4.98471296, 5.393036775, 4.835767372], 'ACTA2': [nan, 7.933184268, 8.301197377, 8.032387589, 8.409755944], 'ACTB': [nan, 14.24293784, 13.91132801, 14.04793914, 13.89475298], 'ACTG1': [nan, 12.8542338, 12.86654373, 12.70595237, 12.66280539], 'ACTL10': [nan, 4.835121939, 4.522425904, 5.063715087, 5.010514063], 'ACTL6A': [nan, 8.47381837, 8.204779345, 7.959905804, 8.384786622], 'ACTMAP': [nan, 7.11952056, 6.541444687, 6.721837077, 6.423744624], 'ACTN1': [nan, 10.26002177, 11.745852, 11.29958065, 11.80234551], 'ACTN4': [nan, 8.849013011, 9.112442232, 9.513798392, 9.127083782], 'ACTR10': [nan, 9.26383082, 9.22458367, 8.954796165, 9.226664991], 'ACTR1A': [nan, 9.384792151, 9.337652357, 9.527139981, 9.236588628], 'ACTR1B': [nan, 8.622598363, 8.373624916, 8.358094448, 8.347839978], 'ACTR2': [nan, 12.29652713, 12.49160898, 11.39986531, 12.24253821], 'ACTR3': [nan, 9.524258083, 10.62159051, 10.04942599, 10.20123556], 'ACTR3B': [nan, 4.824960123, 4.780493059, 4.934962252, 4.843404998], 'ACTR3C': [nan, 4.997944087, 4.607643254, 4.714827021, 4.876399619], 'ACTR5': [nan, 6.817284748, 6.409454607, 6.577555579, 6.634049584], 'ACTR6': [nan, 8.244370887, 8.424263812, 8.661923755, 8.957666718], 'ACTR8': [nan, 5.987179381, 5.955132253, 5.908937968, 6.241966118], 'ACTRT1': [nan, 5.989395174, 5.605908928, 5.55677472, 5.781425629], 'ACVR1': [nan, 8.379842271, 8.806713352, 8.643917348, 8.36831077], 'ACVR1B': [nan, 7.132747792, 6.33226144, 6.023135166, 6.18294161], 'ACVR2A': [nan, 5.752015745, 6.09749957, 6.015993288, 5.796395963], 'ACVRL1': [nan, 6.424035814, 5.403971249, 5.011896236, 5.338285499], 'ACY1': [nan, 6.588303958, 5.508265146, 5.974316035, 5.619026571], 'ACYP1': [nan, 6.007672906, 6.013441501, 6.037500718, 6.186779568], 'ACYP2': [nan, 6.522573048, 5.888982424, 5.605530611, 5.857590529], 'ADA': [nan, 8.40850722, 8.376067211, 8.992276656, 8.639998274], 'ADA2': [nan, 7.95595966, 7.413064994, 7.005587586, 7.194514911], 'ADAM10': [nan, 7.168873731, 6.562272409, 5.497361848, 6.092621029], 'ADAM11': [nan, 4.797681001, 4.746939378, 4.674197118, 4.822591463], 'ADAM12': [nan, 4.613485088, 4.526173239, 4.697676644, 4.835011946], 'ADAM15': [nan, 8.384472011, 6.928883257, 6.784588842, 7.123592181], 'ADAM17': [nan, 7.709929034, 6.966025027, 6.67784572, 6.880284267], 'ADAM19': [nan, 9.604952448, 10.10856454, 9.566360723, 9.713962583], 'ADAM2': [nan, 4.803624965, 4.79276949, 4.967967082, 4.822226303], 'ADAM28': [nan, 5.363854303, 5.300146124, 4.654017643, 4.872022043], 'ADAM29': [nan, 4.832456094, 4.581786814, 4.758329343, 4.541512491], 'ADAM32': [nan, 4.763874102, 4.728202088, 4.867150247, 4.821792362], 'ADAM6': [nan, 5.013728073, 4.454433848, 4.601389614, 4.370063955], 'ADAM8': [nan, 9.050832019, 10.05553307, 10.16783522, 10.09462974], 'ADAM9': [nan, 5.589929496, 4.829724879, 4.501781091, 4.683557313], 'ADAMDEC1': [nan, 5.19819929, 4.484276305, 4.614151772, 4.767802807]}\n", "Linked data shape after handling missing values: (0, 2)\n", "Quartiles for 'Rheumatoid_Arthritis':\n", " 25%: nan\n", " 50% (Median): nan\n", " 75%: nan\n", "Min: nan\n", "Max: nan\n", "The distribution of the feature 'Rheumatoid_Arthritis' in this dataset is fine.\n", "\n", "Quartiles for 'Age':\n", " 25%: nan\n", " 50% (Median): nan\n", " 75%: nan\n", "Min: nan\n", "Max: nan\n", "The distribution of the feature 'Age' in this dataset is fine.\n", "\n", "Abnormality detected in the cohort: GSE97475. Preprocessing failed.\n", "Linked data was not usable and was not saved.\n" ] } ], "source": [ "# 1. Manual creation of clinical features when trait_row is None\n", "sample_columns = clinical_data.columns.drop('!Sample_geo_accession') if '!Sample_geo_accession' in clinical_data.columns else clinical_data.columns\n", "clinical_features = pd.DataFrame(index=[trait, 'Age', 'Gender'])\n", "\n", "# Add constant trait values (all healthy)\n", "clinical_features[sample_columns] = None # Initialize with None\n", "clinical_features.loc[trait, :] = 0 # All are healthy controls\n", "\n", "# Add age data if available\n", "if age_row is not None:\n", " for i, col in enumerate(sample_columns):\n", " if i < len(sample_characteristics_dict.get(age_row, [])):\n", " clinical_features.loc['Age', col] = convert_age(sample_characteristics_dict[age_row][i])\n", "\n", "# Add gender data if available\n", "if gender_row is not None:\n", " for i, col in enumerate(sample_columns):\n", " if i < len(sample_characteristics_dict.get(gender_row, [])):\n", " clinical_features.loc['Gender', col] = convert_gender(sample_characteristics_dict[gender_row][i])\n", "\n", "selected_clinical_data = clinical_features\n", "\n", "print(\"Clinical data preview:\")\n", "print(preview_df(selected_clinical_data))\n", "\n", "# Save the clinical data\n", "os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n", "selected_clinical_data.to_csv(out_clinical_data_file)\n", "print(f\"Clinical data saved to {out_clinical_data_file}\")\n", "\n", "# 2. Normalize the gene symbols and save the gene data\n", "normalized_gene_data = normalize_gene_symbols_in_index(gene_data)\n", "os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)\n", "normalized_gene_data.to_csv(out_gene_data_file)\n", "print(f\"Normalized gene data saved to {out_gene_data_file}\")\n", "\n", "# 3. Link the clinical and genetic data\n", "linked_data = geo_link_clinical_genetic_data(selected_clinical_data, normalized_gene_data)\n", "print(f\"Linked data shape: {linked_data.shape}\")\n", "print(\"Linked data preview:\")\n", "print(preview_df(linked_data))\n", "\n", "# 4. Handle missing values in the linked data\n", "linked_data = handle_missing_values(linked_data, trait)\n", "print(f\"Linked data shape after handling missing values: {linked_data.shape}\")\n", "\n", "# 5. Determine whether the trait and some demographic features are severely biased, and remove biased features\n", "is_trait_biased, unbiased_linked_data = judge_and_remove_biased_features(linked_data, trait)\n", "\n", "# 6. Conduct quality check and save the cohort information\n", "is_usable = validate_and_save_cohort_info(\n", " is_final=True, \n", " cohort=cohort, \n", " info_path=json_path, \n", " is_gene_available=True, \n", " is_trait_available=True, \n", " is_biased=is_trait_biased, \n", " df=unbiased_linked_data,\n", " note=\"All subjects are healthy controls (Hepatitis B vaccine recipients) with no disease status variation\"\n", ")\n", "\n", "# 7. If the linked data is usable, save it as a CSV file\n", "if is_usable:\n", " os.makedirs(os.path.dirname(out_data_file), exist_ok=True)\n", " unbiased_linked_data.to_csv(out_data_file)\n", " print(f\"Usable linked data saved to {out_data_file}\")\n", "else:\n", " print(\"Linked data was not usable and was not saved.\")" ] } ], "metadata": { "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.16" } }, "nbformat": 4, "nbformat_minor": 5 }