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scripts/parse_hughes_2006.R

@@ -4,12 +4,12 @@ library(arrow)
 library(readxl)
 
 # Constants ----
-GENOMIC_FEATURES_PATH <- here("data/genome_files/hf/features")
+genomicfeatures_PATH <- here("data/genome_files/hf/features")
 HUGHES_DATA_DIR <- here("data/hughes_2006")
 
 # Load genomic features harmonization table ----
 # See https://huggingface.co/datasets/BrentLab/yeast_genome_resources
-genomicfeatures <- arrow::open_dataset(GENOMIC_FEATURES_PATH) %>%
+genomicfeatures <- arrow::open_dataset(genomicfeatures_PATH) %>%
   as_tibble()
 
 #' Read and process Hughes normalized data
@@ -140,13 +140,13 @@ validate_data_consistency <- function() {
   tests <- list(
     # Check regulator locus tags match genomic features
     regulator_locus_consistency = setequal(
-      intersect(genomic_features$locus_tag, hughes_2006_meta$regulator_locus_tag),
+      intersect(genomicfeatures$locus_tag, hughes_2006_meta$regulator_locus_tag),
       hughes_2006_meta$regulator_locus_tag
     ),
 
     # Check regulator symbols match genomic features
     regulator_symbol_consistency = setequal(
-      intersect(genomic_features$symbol, hughes_2006_meta$regulator_symbol),
+      intersect(genomicfeatures$symbol, hughes_2006_meta$regulator_symbol),
       hughes_2006_meta$regulator_symbol
     ),
 
@@ -171,7 +171,7 @@ validate_data_consistency <- function() {
     # Check targets match genomic features
     target_genomic_consistency = setequal(
       unique(df_oe$hughes_target),
-      intersect(unique(df_oe$hughes_target), genomic_features$locus_tag)
+      intersect(unique(df_oe$hughes_target), genomicfeatures$locus_tag)
     )
   )
 
@@ -205,16 +205,16 @@ if (missing_targets_count > 0) {
 
 missing_locus_tags <- setdiff(
   unique(df_oe$hughes_target),
-  intersect(unique(df_oe$hughes_target), genomic_features$locus_tag)
+  intersect(unique(df_oe$hughes_target), genomicfeatures$locus_tag)
 )
 
 genome_map = tibble(
   locus_tag = intersect(unique(df_oe$hughes_target),
-                        genomic_features$locus_tag)) %>%
+                        genomicfeatures$locus_tag)) %>%
   left_join(genomicfeatures %>% select(locus_tag, symbol)) %>%
   mutate(hughes_target = locus_tag) %>%
   bind_rows(
-    genomic_features %>%
+    genomicfeatures %>%
       filter(str_detect(alias, paste(missing_locus_tags, collapse = "|"))) %>%
       mutate(alias_match = str_extract(alias, paste(missing_locus_tags, collapse = "|"))) %>%
       dplyr::rename(hughes_target = alias_match) %>%
@@ -224,21 +224,59 @@ genome_map = tibble(
 
 stopifnot(setequal(genome_map$hughes_target, unique(df_oe$hughes_target)))
 
-df_oe_harmonized =
-  df_oe %>%
-  select(-c(sample, regulator_symbol)) %>%
-  pivot_wider(id_cols = c(regulator_symbol, hughes_target),
-              names_from = dye_orientation,
-              values_from = norm_log2fc) %>%
-  dplyr::rename(dye_plus = `+`, dye_minus = `-`) %>%
-  left_join(df_oe)
+df_oe_harmonized = df_oe %>%
   left_join(
     select(hughes_2006_meta,
            regulator_locus_tag,
-           regulator_symbol) %>%
+           regulator_symbol)) %>%
   left_join(genome_map) %>%
   select(regulator_locus_tag, regulator_symbol,
          target_locus_tag, target_symbol,
-         mean_log2fc)
+         dye_plus, dye_minus, mean_norm_log2fc)
 
+df_oe_harmonized %>%
+  write_parquet("~/code/hf/hughes_2006/overexpression.parquet",
+                compression = "zstd",
+                write_statistics = TRUE,
+                use_dictionary = c(
+                  regulator_locus_tag = TRUE,
+                  regulator_symbol = TRUE,
+                  target_locus_tag = TRUE,
+                  target_symbol = TRUE
+                )
+  )
 
+df_ko_harmonized = df_ko %>%
+  left_join(
+    select(hughes_2006_meta,
+           regulator_locus_tag,
+           regulator_symbol)) %>%
+  left_join(genome_map) %>%
+  select(regulator_locus_tag, regulator_symbol,
+         target_locus_tag, target_symbol,
+         dye_plus, dye_minus, mean_norm_log2fc)
+
+df_ko_harmonized %>%
+  write_parquet("~/code/hf/hughes_2006/knockout.parquet",
+                compression = "zstd",
+                write_statistics = TRUE,
+                use_dictionary = c(
+                  regulator_locus_tag = TRUE,
+                  regulator_symbol = TRUE,
+                  target_locus_tag = TRUE,
+                  target_symbol = TRUE
+                )
+  )
+
+hughes_2006_meta %>%
+  janitor::clean_names() %>%
+  write_parquet("~/code/hf/hughes_2006/metadata.parquet",
+                compression = "zstd",
+                write_statistics = TRUE,
+                use_dictionary = c(
+                  regulator_locus_tag = TRUE,
+                  regulator_symbol = TRUE,
+                  oe_passed_qc = TRUE,
+                  del_passed_qc = TRUE
+                )
+  )