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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "28b6d53b",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:27:13.344866Z",
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"shell.execute_reply": "2025-03-25T06:27:13.501543Z"
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},
"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 = \"Alzheimers_Disease\"\n",
"cohort = \"GSE214417\"\n",
"\n",
"# Input paths\n",
"in_trait_dir = \"../../input/GEO/Alzheimers_Disease\"\n",
"in_cohort_dir = \"../../input/GEO/Alzheimers_Disease/GSE214417\"\n",
"\n",
"# Output paths\n",
"out_data_file = \"../../output/preprocess/Alzheimers_Disease/GSE214417.csv\"\n",
"out_gene_data_file = \"../../output/preprocess/Alzheimers_Disease/gene_data/GSE214417.csv\"\n",
"out_clinical_data_file = \"../../output/preprocess/Alzheimers_Disease/clinical_data/GSE214417.csv\"\n",
"json_path = \"../../output/preprocess/Alzheimers_Disease/cohort_info.json\"\n"
]
},
{
"cell_type": "markdown",
"id": "f46457a6",
"metadata": {},
"source": [
"### Step 1: Initial Data Loading"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "d4e4aa21",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:27:13.503463Z",
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"shell.execute_reply": "2025-03-25T06:27:13.594401Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Background Information:\n",
"!Series_title\t\"Long-term Urolithin A treatment ameliorates disease pathology in Alzheimer's Disease mouse models\"\n",
"!Series_summary\t\"This SuperSeries is composed of the SubSeries listed below.\"\n",
"!Series_overall_design\t\"Refer to individual Series\"\n",
"Sample Characteristics Dictionary:\n",
"{0: ['tissue: hippocampus'], 1: ['treatment: water', 'treatment: Urolithin A_5m', 'treatment: water+washout', 'treatment: Urolithin A_5m+washout_1m'], 2: ['Sex: Male'], 3: ['age: 8 months', 'age: 9 months'], 4: ['strain: B6.Cg-Tg(APPswe,PSEN1dE9)85Dbo/J'], 5: ['genotype: - APP - PSEN', 'genotype: + APP + PSEN']}\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": "6da67395",
"metadata": {},
"source": [
"### Step 2: Dataset Analysis and Clinical Feature Extraction"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "73c7f4f8",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:27:13.596645Z",
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"iopub.status.idle": "2025-03-25T06:27:13.606750Z",
"shell.execute_reply": "2025-03-25T06:27:13.606194Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Clinical Features Preview:\n",
"{'GSM6567822': [0.0, 8.0], 'GSM6567823': [0.0, 8.0], 'GSM6567824': [0.0, 8.0], 'GSM6567825': [0.0, 8.0], 'GSM6567826': [1.0, 8.0], 'GSM6567827': [1.0, 8.0], 'GSM6567828': [1.0, 8.0], 'GSM6567829': [1.0, 8.0], 'GSM6567830': [1.0, 8.0], 'GSM6567831': [1.0, 8.0], 'GSM6567832': [1.0, 8.0], 'GSM6567833': [0.0, 9.0], 'GSM6567834': [0.0, 9.0], 'GSM6567835': [0.0, 9.0], 'GSM6567836': [0.0, 9.0], 'GSM6567837': [0.0, 9.0], 'GSM6567838': [1.0, 9.0], 'GSM6567839': [1.0, 9.0], 'GSM6567840': [1.0, 9.0], 'GSM6567841': [1.0, 9.0], 'GSM6567842': [1.0, 9.0], 'GSM6567843': [1.0, 9.0], 'GSM6567844': [1.0, 9.0], 'GSM6567845': [1.0, 9.0]}\n",
"Clinical features saved to ../../output/preprocess/Alzheimers_Disease/clinical_data/GSE214417.csv\n"
]
}
],
"source": [
"import pandas as pd\n",
"import os\n",
"import json\n",
"from typing import Optional, Callable, Dict, Any\n",
"\n",
"# 1. Gene Expression Data Availability\n",
"# Looking at the background information, this appears to be gene expression data from mouse models of Alzheimer's disease\n",
"is_gene_available = True\n",
"\n",
"# 2. Variable Availability and Data Type Conversion\n",
"# 2.1 Data Availability\n",
"# For trait, we can use the genotype information (key 5) which distinguishes AD vs control mice\n",
"trait_row = 5 # 'genotype: - APP - PSEN' vs 'genotype: + APP + PSEN'\n",
"\n",
"# Age information is available at key 3\n",
"age_row = 3 # 'age: 8 months', 'age: 9 months'\n",
"\n",
"# Gender information is available at key 2, but it's a constant (all Male)\n",
"gender_row = None # Only one value 'Sex: Male', so it's not useful for association studies\n",
"\n",
"# 2.2 Data Type Conversion Functions\n",
"def convert_trait(value):\n",
" if value is None:\n",
" return None\n",
" # Extract the part after the colon\n",
" if ':' in value:\n",
" value = value.split(':', 1)[1].strip()\n",
" \n",
" # The genotype with \"+\" indicates Alzheimer's disease model, \"-\" indicates control\n",
" if '+ APP + PSEN' in value:\n",
" return 1 # AD model\n",
" elif '- APP - PSEN' in value:\n",
" return 0 # Control\n",
" else:\n",
" return None\n",
"\n",
"def convert_age(value):\n",
" if value is None:\n",
" return None\n",
" # Extract the part after the colon\n",
" if ':' in value:\n",
" value = value.split(':', 1)[1].strip()\n",
" \n",
" # Extract the numeric age in months\n",
" if 'months' in value or 'month' in value:\n",
" try:\n",
" # Extract just the number\n",
" age_value = value.split()[0]\n",
" return float(age_value)\n",
" except (ValueError, IndexError):\n",
" return None\n",
" return None\n",
"\n",
"# Not used but defined for completeness\n",
"def convert_gender(value):\n",
" if value is None:\n",
" return None\n",
" # Extract the part after the colon\n",
" if ':' in value:\n",
" value = value.split(':', 1)[1].strip()\n",
" \n",
" value = value.lower()\n",
" if 'female' in value:\n",
" return 0\n",
" elif 'male' in value:\n",
" return 1\n",
" else:\n",
" return None\n",
"\n",
"# 3. Save Metadata\n",
"is_trait_available = trait_row is not None\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",
"# Since trait_row is not None, we need to extract clinical features\n",
"if trait_row is not None:\n",
" # Assume clinical_data is already defined from a previous step\n",
" # If not, we would need to load it\n",
" try:\n",
" # Load clinical data if it's not already available\n",
" clinical_data_file = os.path.join(in_cohort_dir, \"clinical_data.csv\")\n",
" if 'clinical_data' not in locals():\n",
" clinical_data = pd.read_csv(clinical_data_file)\n",
" \n",
" # Extract clinical features\n",
" clinical_features = geo_select_clinical_features(\n",
" clinical_df=clinical_data,\n",
" trait=trait,\n",
" trait_row=trait_row,\n",
" convert_trait=convert_trait,\n",
" age_row=age_row,\n",
" convert_age=convert_age\n",
" # gender_row and convert_gender are None since gender is constant\n",
" )\n",
" \n",
" # Preview the extracted clinical features\n",
" preview = preview_df(clinical_features)\n",
" print(\"Clinical Features Preview:\")\n",
" print(preview)\n",
" \n",
" # Create the directory if it doesn't exist\n",
" os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n",
" \n",
" # Save the clinical features to a CSV file\n",
" clinical_features.to_csv(out_clinical_data_file, index=False)\n",
" print(f\"Clinical features saved to {out_clinical_data_file}\")\n",
" except Exception as e:\n",
" print(f\"Error in clinical feature extraction: {str(e)}\")\n"
]
},
{
"cell_type": "markdown",
"id": "5b5dbbe8",
"metadata": {},
"source": [
"### Step 3: Gene Data Extraction"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "7b8cc1fc",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:27:13.608438Z",
"iopub.status.busy": "2025-03-25T06:27:13.608298Z",
"iopub.status.idle": "2025-03-25T06:27:13.706600Z",
"shell.execute_reply": "2025-03-25T06:27:13.705958Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"First 20 gene/probe identifiers:\n",
"Index(['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13',\n",
" '14', '15', '16', '17', '18', '19', '20'],\n",
" dtype='object', name='ID')\n"
]
}
],
"source": [
"# 1. First get the file paths again to access the matrix file\n",
"soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
"\n",
"# 2. Use the get_genetic_data function from the library to get the gene_data from the matrix_file\n",
"gene_data = get_genetic_data(matrix_file)\n",
"\n",
"# 3. Print the first 20 row IDs (gene or probe identifiers) for future observation\n",
"print(\"First 20 gene/probe identifiers:\")\n",
"print(gene_data.index[:20])\n"
]
},
{
"cell_type": "markdown",
"id": "a2107889",
"metadata": {},
"source": [
"### Step 4: Gene Identifier Review"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "276a1ca7",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:27:13.708387Z",
"iopub.status.busy": "2025-03-25T06:27:13.708276Z",
"iopub.status.idle": "2025-03-25T06:27:13.710989Z",
"shell.execute_reply": "2025-03-25T06:27:13.710461Z"
}
},
"outputs": [],
"source": [
"# The identifiers are numeric values (1, 2, 3, etc.) and not human gene symbols\n",
"# These appear to be row numbers or possibly probe IDs that need to be mapped to actual gene symbols\n",
"\n",
"requires_gene_mapping = True\n"
]
},
{
"cell_type": "markdown",
"id": "c261031d",
"metadata": {},
"source": [
"### Step 5: Gene Annotation"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "4af777e6",
"metadata": {
"execution": {
"iopub.execute_input": "2025-03-25T06:27:13.712646Z",
"iopub.status.busy": "2025-03-25T06:27:13.712543Z",
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"shell.execute_reply": "2025-03-25T06:27:16.387518Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Gene annotation preview:\n",
"{'ID': ['1', '2', '3', '4', '5'], 'COL': ['192', '192', '192', '192', '192'], 'ROW': ['328', '326', '324', '322', '320'], 'NAME': ['GE_BrightCorner', 'DarkCorner', 'DarkCorner', 'A_51_P399985', 'A_55_P2508138'], 'SPOT_ID': ['CONTROL', 'CONTROL', 'CONTROL', nan, nan], 'CONTROL_TYPE': ['pos', 'pos', 'pos', 'FALSE', 'FALSE'], 'REFSEQ': [nan, nan, nan, 'NM_015742', 'NR_028378'], 'GB_ACC': [nan, nan, nan, 'NM_015742', 'NR_028378'], 'LOCUSLINK_ID': [nan, nan, nan, 17925.0, 100034739.0], 'GENE_SYMBOL': [nan, nan, nan, 'Myo9b', 'Gm17762'], 'GENE_NAME': [nan, nan, nan, 'myosin IXb', 'predicted gene, 17762'], 'UNIGENE_ID': [nan, nan, nan, 'Mm.33779', 'Mm.401643'], 'ENSEMBL_ID': [nan, nan, nan, 'ENSMUST00000170242', nan], 'ACCESSION_STRING': [nan, nan, nan, 'ref|NM_015742|ref|NM_001142322|ref|NM_001142323|ens|ENSMUST00000170242', 'ref|NR_028378|gb|AK171729|gb|AK045818|gb|AK033161'], 'CHROMOSOMAL_LOCATION': [nan, nan, nan, 'chr8:73884459-73884518', 'chr2:17952143-17952202'], 'CYTOBAND': [nan, nan, nan, 'mm|8qB3.3', 'mm|2qA3'], 'DESCRIPTION': [nan, nan, nan, 'Mus musculus myosin IXb (Myo9b), transcript variant 3, mRNA [NM_015742]', 'Mus musculus predicted gene, 17762 (Gm17762), long non-coding RNA [NR_028378]'], 'GO_ID': [nan, nan, nan, 'GO:0000146(microfilament motor activity)|GO:0000166(nucleotide binding)|GO:0001726(ruffle)|GO:0002548(monocyte chemotaxis)|GO:0003774(motor activity)|GO:0003779(actin binding)|GO:0005096(GTPase activator activity)|GO:0005516(calmodulin binding)|GO:0005524(ATP binding)|GO:0005622(intracellular)|GO:0005737(cytoplasm)|GO:0005856(cytoskeleton)|GO:0005884(actin filament)|GO:0005938(cell cortex)|GO:0007165(signal transduction)|GO:0007266(Rho protein signal transduction)|GO:0008152(metabolic process)|GO:0008270(zinc ion binding)|GO:0016020(membrane)|GO:0016459(myosin complex)|GO:0016887(ATPase activity)|GO:0030010(establishment of cell polarity)|GO:0030027(lamellipodium)|GO:0030898(actin-dependent ATPase activity)|GO:0031941(filamentous actin)|GO:0032433(filopodium tip)|GO:0033275(actin-myosin filament sliding)|GO:0035556(intracellular signal transduction)|GO:0043008(ATP-dependent protein binding)|GO:0043531(ADP binding)|GO:0043547(positive regulation of GTPase activity)|GO:0046872(metal ion binding)|GO:0048246(macrophage chemotaxis)|GO:0048471(perinuclear region of cytoplasm)|GO:0051015(actin filament binding)|GO:0072673(lamellipodium morphogenesis)', nan], 'SEQUENCE': [nan, nan, nan, 'ACGGAGCCAGGGACTTGGAACCTTTAGGAACAATCAGTGCATCCGGTGACAGCCTGGGTT', 'GGAAAGTACTTCAGCTTCACTCTTTAATTCTCCTTTACTACAATTAAAACTTTCGGTCAG'], 'SPOT_ID.1': [nan, nan, nan, nan, nan]}\n"
]
}
],
"source": [
"# 1. First get the file paths using geo_get_relevant_filepaths function\n",
"soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
"\n",
"# 2. Use the 'get_gene_annotation' function from the library to get gene annotation data from the SOFT file.\n",
"gene_annotation = get_gene_annotation(soft_file)\n",
"\n",
"# 3. Use the 'preview_df' function from the library to preview the data and print out the results.\n",
"print(\"Gene annotation preview:\")\n",
"print(preview_df(gene_annotation))\n"
]
},
{
"cell_type": "markdown",
"id": "cb8600fe",
"metadata": {},
"source": [
"### Step 6: Gene Identifier Mapping"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "18b90c7d",
"metadata": {
"execution": {
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"shell.execute_reply": "2025-03-25T06:27:16.540769Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Mapped gene expression data (first 5 genes):\n",
" GSM6567822 GSM6567823 GSM6567824 GSM6567825 GSM6567826 \\\n",
"Gene \n",
"A130033P14 -0.24 -0.18 -0.21 -0.30 -0.23 \n",
"A230055C15 0.25 0.45 0.41 0.32 0.39 \n",
"A330044H09 0.85 0.91 0.90 0.78 0.90 \n",
"A430057O09 -1.21 -1.04 -1.26 -1.15 -1.19 \n",
"A430085C19 -0.68 -0.95 -0.83 -0.89 -0.92 \n",
"\n",
" GSM6567827 GSM6567828 GSM6567829 GSM6567830 GSM6567831 ... \\\n",
"Gene ... \n",
"A130033P14 -0.18 -0.20 -0.19 -0.16 -0.18 ... \n",
"A230055C15 0.33 0.37 0.39 0.41 0.41 ... \n",
"A330044H09 0.91 0.87 0.90 0.82 0.91 ... \n",
"A430057O09 -1.22 -1.09 -1.21 -1.23 -1.19 ... \n",
"A430085C19 -0.62 -0.88 -0.90 -0.95 -1.12 ... \n",
"\n",
" GSM6567836 GSM6567837 GSM6567838 GSM6567839 GSM6567840 \\\n",
"Gene \n",
"A130033P14 -0.40 -0.23 -0.31 -0.24 -0.34 \n",
"A230055C15 0.38 0.44 0.24 0.19 0.29 \n",
"A330044H09 0.87 0.94 0.85 0.86 1.01 \n",
"A430057O09 -1.21 -1.21 -0.97 -1.32 -1.27 \n",
"A430085C19 -1.19 -0.88 -0.95 -1.10 0.00 \n",
"\n",
" GSM6567841 GSM6567842 GSM6567843 GSM6567844 GSM6567845 \n",
"Gene \n",
"A130033P14 -0.35 -0.34 0.38 -0.18 -0.25 \n",
"A230055C15 0.20 0.22 0.13 0.12 0.19 \n",
"A330044H09 0.78 0.81 0.80 0.84 0.82 \n",
"A430057O09 -1.30 -1.17 -1.11 -1.17 -1.21 \n",
"A430085C19 -1.33 -1.19 -1.11 -1.20 -1.23 \n",
"\n",
"[5 rows x 24 columns]\n",
"Shape of mapped gene expression data: (511, 24)\n"
]
}
],
"source": [
"# 1. Identify the appropriate columns in gene_annotation for mapping\n",
"# The gene expression data uses numeric identifiers that correspond to the 'ID' column\n",
"# The gene symbols are stored in the 'GENE_SYMBOL' column\n",
"\n",
"# 2. Create gene mapping dataframe using the get_gene_mapping function\n",
"gene_mapping = get_gene_mapping(gene_annotation, 'ID', 'GENE_SYMBOL')\n",
"\n",
"# 3. Apply the gene mapping to convert probe-level measurements to gene expression data\n",
"# The apply_gene_mapping function handles the many-to-many relationship as described\n",
"gene_data = apply_gene_mapping(gene_data, gene_mapping)\n",
"\n",
"# Preview the mapped gene expression data\n",
"print(\"Mapped gene expression data (first 5 genes):\")\n",
"print(gene_data.head(5))\n",
"print(f\"Shape of mapped gene expression data: {gene_data.shape}\")\n"
]
},
{
"cell_type": "markdown",
"id": "e5d249dc",
"metadata": {},
"source": [
"### Step 7: Data Normalization and Linking"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "9a917ea7",
"metadata": {
"execution": {
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"shell.execute_reply": "2025-03-25T06:27:16.697215Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Normalizing gene symbols...\n"
]
},
{
"name": "stdout",
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"text": [
"Gene data shape after normalization: (30, 24)\n",
"Normalized gene data saved to ../../output/preprocess/Alzheimers_Disease/gene_data/GSE214417.csv\n",
"Loading the original clinical data...\n",
"Extracting clinical features...\n",
"Clinical data preview:\n",
"{'GSM6567822': [0.0, 8.0], 'GSM6567823': [0.0, 8.0], 'GSM6567824': [0.0, 8.0], 'GSM6567825': [0.0, 8.0], 'GSM6567826': [1.0, 8.0], 'GSM6567827': [1.0, 8.0], 'GSM6567828': [1.0, 8.0], 'GSM6567829': [1.0, 8.0], 'GSM6567830': [1.0, 8.0], 'GSM6567831': [1.0, 8.0], 'GSM6567832': [1.0, 8.0], 'GSM6567833': [0.0, 9.0], 'GSM6567834': [0.0, 9.0], 'GSM6567835': [0.0, 9.0], 'GSM6567836': [0.0, 9.0], 'GSM6567837': [0.0, 9.0], 'GSM6567838': [1.0, 9.0], 'GSM6567839': [1.0, 9.0], 'GSM6567840': [1.0, 9.0], 'GSM6567841': [1.0, 9.0], 'GSM6567842': [1.0, 9.0], 'GSM6567843': [1.0, 9.0], 'GSM6567844': [1.0, 9.0], 'GSM6567845': [1.0, 9.0]}\n",
"Clinical data saved to ../../output/preprocess/Alzheimers_Disease/clinical_data/GSE214417.csv\n",
"Linking clinical and genetic data...\n",
"Linked data shape: (24, 32)\n",
"Handling missing values...\n",
"Linked data shape after handling missing values: (24, 32)\n",
"Checking for bias in trait distribution...\n",
"For the feature 'Alzheimers_Disease', the least common label is '0.0' with 9 occurrences. This represents 37.50% of the dataset.\n",
"The distribution of the feature 'Alzheimers_Disease' in this dataset is fine.\n",
"\n",
"Quartiles for 'Age':\n",
" 25%: 8.0\n",
" 50% (Median): 9.0\n",
" 75%: 9.0\n",
"Min: 8.0\n",
"Max: 9.0\n",
"The distribution of the feature 'Age' in this dataset is fine.\n",
"\n",
"Dataset usability: True\n",
"Linked data saved to ../../output/preprocess/Alzheimers_Disease/GSE214417.csv\n"
]
}
],
"source": [
"# 1. Normalize gene symbols in the gene expression data\n",
"print(\"Normalizing gene symbols...\")\n",
"normalized_gene_data = normalize_gene_symbols_in_index(gene_data)\n",
"print(f\"Gene data shape after normalization: {normalized_gene_data.shape}\")\n",
"\n",
"# Save the normalized gene data to a CSV file\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",
"# 2. Link the clinical and genetic data\n",
"print(\"Loading the original clinical data...\")\n",
"# Get the matrix file again to ensure we have the proper data\n",
"soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)\n",
"background_info, clinical_data = get_background_and_clinical_data(matrix_file)\n",
"\n",
"print(\"Extracting clinical features...\")\n",
"# Use the clinical_data obtained directly from the matrix file\n",
"selected_clinical_df = geo_select_clinical_features(\n",
" clinical_df=clinical_data,\n",
" trait=trait,\n",
" trait_row=trait_row,\n",
" convert_trait=convert_trait,\n",
" age_row=age_row,\n",
" convert_age=convert_age,\n",
" gender_row=gender_row,\n",
" convert_gender=convert_gender\n",
")\n",
"\n",
"print(\"Clinical data preview:\")\n",
"print(preview_df(selected_clinical_df))\n",
"\n",
"# Save the clinical data to a CSV file\n",
"os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)\n",
"selected_clinical_df.to_csv(out_clinical_data_file)\n",
"print(f\"Clinical data saved to {out_clinical_data_file}\")\n",
"\n",
"# Link clinical and genetic data using the normalized gene data\n",
"print(\"Linking clinical and genetic data...\")\n",
"linked_data = geo_link_clinical_genetic_data(selected_clinical_df, normalized_gene_data)\n",
"print(f\"Linked data shape: {linked_data.shape}\")\n",
"\n",
"# 3. Handle missing values in the linked data\n",
"print(\"Handling missing values...\")\n",
"linked_data = handle_missing_values(linked_data, trait)\n",
"print(f\"Linked data shape after handling missing values: {linked_data.shape}\")\n",
"\n",
"# 4. Check if trait is biased\n",
"print(\"Checking for bias in trait distribution...\")\n",
"is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)\n",
"\n",
"# 5. Final validation\n",
"note = \"Dataset contains gene expression data from bronchial brushings from control individuals and patients with asthma after rhinovirus infection in vivo, as described in the study 'Rhinovirus-induced epithelial RIG-I inflammasome suppresses antiviral immunity and promotes inflammation in asthma and COVID-19'.\"\n",
"is_usable = validate_and_save_cohort_info(\n",
" is_final=True,\n",
" cohort=cohort,\n",
" info_path=json_path,\n",
" is_gene_available=is_gene_available,\n",
" is_trait_available=is_trait_available,\n",
" is_biased=is_biased,\n",
" df=linked_data,\n",
" note=note\n",
")\n",
"\n",
"print(f\"Dataset usability: {is_usable}\")\n",
"\n",
"# 6. Save linked data if usable\n",
"if is_usable:\n",
" os.makedirs(os.path.dirname(out_data_file), exist_ok=True)\n",
" linked_data.to_csv(out_data_file)\n",
" print(f\"Linked data saved to {out_data_file}\")\n",
"else:\n",
" print(\"Dataset is not usable for trait-gene association studies due to bias or other issues.\")"
]
}
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