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scripts/parse_mahendrawada.R

@@ -3,6 +3,12 @@ library(here)
 library(arrow)
 library(readxl)
 
+# from fetchngs, the multiqc metadata has an easy way to map between
+# accessions and samples
+multqc_chec_config = yaml::read_yaml("~/Downloads/multiqc_config.yml")
+chec_meta <- map_dfr(multqc_chec_config$sample_names_rename,
+             ~tibble(!!!setNames(., multqc_chec_config$sample_names_rename_buttons)))
+
 # genomic feature harmonization table ----
 # see https://huggingface.co/datasets/BrentLab/yeast_genome_resources
 genomicfeatures = arrow::open_dataset(here("data/genome_files/hf/features")) %>%
@@ -90,24 +96,6 @@ stopifnot(
     filter(!complete.cases(.) | locus_tag != gene_id) %>%
     nrow() == 0)
 
-mahedrawada_genomicfeatures %>%
-  left_join(genomicfeatures %>%
-              select(locus_tag, symbol) %>%
-              mutate(gene_id = locus_tag)) %>%
-  write_parquet(here("~/code/hf/mahendrawada_2025/features_mahendrawada_2025.parquet"),
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  gene_id = TRUE,
-                  gene_name = TRUE,
-                  chr = TRUE,
-                  locus_tag = TRUE,
-                  symbol = TRUE,
-                  coactivator = TRUE
-                )
-  )
-
-
 chec_data_final = chec_data %>%
   left_join(
     genomicfeatures %>%
@@ -122,18 +110,6 @@ chec_data_final = chec_data %>%
   select(regulator_locus_tag, regulator_symbol, target_locus_tag, target_symbol, peak_score) %>%
   arrange(regulator_locus_tag, target_locus_tag)
 
-chec_data_final %>%
-  write_parquet(here("~/code/hf/mahendrawada_2025/chec_mahendrawada_2025.parquet"),
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE,
-                  target_locus_tag = TRUE,
-                  target_symbol = TRUE
-                )
-  )
-
 rnaseq_data_final = rnaseq_data %>%
   left_join(
     genomicfeatures %>%
@@ -148,14 +124,55 @@ rnaseq_data_final = rnaseq_data %>%
   select(regulator_locus_tag, regulator_symbol, target_locus_tag, target_symbol, log2fc) %>%
   arrange(regulator_locus_tag, target_locus_tag)
 
-rnaseq_data_final %>%
-  write_parquet(here("~/code/hf/mahendrawada_2025/rnaseq_mahendrawada_2025.parquet"),
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE,
-                  target_locus_tag = TRUE,
-                  target_symbol = TRUE
-                )
-  )
+sample_id_map = tibble(
+  regulator_locus_tag = union(rnaseq_data_final$regulator_locus_tag,
+                                     chec_data_final$regulator_locus_tag)) %>%
+  mutate(sample_id = row_number())
+
+
+# chec_data_final %>%
+#   left_join(sample_id_map) %>%
+#   select(sample_id, all_of(colnames(chec_data_final))) %>%
+#   write_parquet(here("~/code/hf/mahendrawada_2025/chec_mahendrawada_2025.parquet"),
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   target_locus_tag = TRUE,
+#                   target_symbol = TRUE
+#                 )
+#   )
+#
+# rnaseq_data_final %>%
+#   left_join(sample_id_map) %>%
+#   select(sample_id, all_of(colnames(rnaseq_data_final))) %>%
+#   write_parquet(here("~/code/hf/mahendrawada_2025/rnaseq_mahendrawada_2025.parquet"),
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   target_locus_tag = TRUE,
+#                   target_symbol = TRUE
+#                 )
+#   )
+#
+# mahedrawada_genomicfeatures %>%
+#   left_join(genomicfeatures %>%
+#               select(locus_tag, symbol) %>%
+#               mutate(gene_id = locus_tag)) %>%
+#   write_parquet(here("~/code/hf/mahendrawada_2025/features_mahendrawada_2025.parquet"),
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   gene_id = TRUE,
+#                   gene_name = TRUE,
+#                   chr = TRUE,
+#                   locus_tag = TRUE,
+#                   symbol = TRUE,
+#                   coactivator = TRUE
+#                 )
+#   )