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scripts/parse_barkai_checseq.R

@@ -170,18 +170,11 @@ gse178430_parsed_meta = bind_cols(
                 regulator_symbol = mnase_tagged_symbol) %>%
   select(accession, regulator_locus_tag, regulator_symbol, strainid,
          instrument, genotype, dbd_donor_symbol, ortholog_donor,
-         paralog_deletion_symbol, paralog_resistance_cassette)
-
-gse178430_parsed_meta %>%
-  write_parquet(here("/home/chase/code/hf/barkai_compendium/GSE178430_metadata.parquet"),
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  accession = TRUE,
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE
-                )
-  )
+         paralog_deletion_symbol, paralog_resistance_cassette) %>%
+  arrange(accession) %>%
+  mutate(series = "GSE178430") %>%
+  mutate(sample_id = row_number()) %>%
+  relocate(sample_id, series, accession)
 
 gse209631_meta = read_csv("data/barkai_checseq/GSE209631/SraRunTable.csv")
 
@@ -192,37 +185,75 @@ gse209631_parsed_meta = gse209631_meta %>%
   arrange(tagged_tf, variant_type) %>%
   left_join(select(genomicfeatures, locus_tag, symbol) %>% dplyr::rename(tagged_tf = symbol)) %>%
   dplyr::rename(regulator_symbol = tagged_tf, regulator_locus_tag = locus_tag) %>%
-  select(accession, regulator_locus_tag, regulator_symbol, variant_type)
-
-gse209631_parsed_meta %>%
-  write_parquet(here("/home/chase/code/hf/barkai_compendium/GSE209631_metadata.parquet"),
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  accession = TRUE,
-                  regulator_locus_tag = TRUE,
-                  regulator_symbol = TRUE,
-                  variant_type = TRUE
-                )
-  )
+  select(accession, regulator_locus_tag, regulator_symbol, variant_type) %>%
+  arrange(accession) %>%
+  mutate(series = "GSE209631") %>%
+  mutate(sample_id = row_number()) %>%
+  relocate(sample_id, series, accession)
+
+
 
-gse=GEOquery::getGEO(filename=here("data/barkai_checseq/GSE222268_series_matrix.txt"))
+gse222268 = GEOquery::getGEO(filename=here("data/barkai_checseq/GSE222268_series_matrix.txt"))
 
-gse222268_meta = Biobase::pData(gse@phenoData) %>% as_tibble() %>%
+gse222268_meta = Biobase::pData(gse222268@phenoData) %>% as_tibble() %>%
   select(title, geo_accession, extract_protocol_ch1, description,
          instrument_model, library_selection) %>%
   mutate(description = ifelse(description == "", library_selection, description)) %>%
   dplyr::rename(accession = geo_accession) %>%
   select(-library_selection, -instrument_model, -extract_protocol_ch1)
 
-gse222268_meta %>%
-  write_parquet(here("/home/chase/code/hf/barkai_compendium/GSE222268_metadata.parquet"),
-                compression = "zstd",
-                write_statistics = TRUE,
-                use_dictionary = c(
-                  accession = TRUE
-                )
-  )
-
-
-
+gse222268_parsed_meta <- gse222268_meta %>%
+  mutate(
+    regulator_symbol = str_extract(title, "^[^_]+"),
+    experiment_details = str_remove(title, "^[^_]+_")) %>%
+  mutate(regulator_symbol = toupper(regulator_symbol)) %>%
+  mutate(regulator_symbol = str_replace(regulator_symbol, "UGA3C", "UGA3")) %>%
+  mutate(regulator_symbol = ifelse(str_detect(regulator_symbol, "MNASE"),
+                                   "none", regulator_symbol)) %>%
+  left_join(
+    select(genomicfeatures, locus_tag, symbol) %>%
+      dplyr::rename(regulator_locus_tag = locus_tag,
+                    regulator_symbol = symbol)) %>%
+  replace_na(list(regulator_locus_tag = "none")) %>%
+  select(-title) %>%
+  arrange(accession) %>%
+  mutate(series = "GSE222268") %>%
+  mutate(sample_id = row_number()) %>%
+  relocate(sample_id, series, accession)
+
+# gse178430_parsed_meta %>%
+#   write_parquet(here("/home/chase/code/hf/barkai_compendium/GSE178430_metadata.parquet"),
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   accession = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE
+#                 )
+#   )
+#
+# gse209631_parsed_meta %>%
+#   write_parquet(here("/home/chase/code/hf/barkai_compendium/GSE209631_metadata.parquet"),
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   accession = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   variant_type = TRUE
+#                 )
+#   )
+#
+# gse222268_parsed_meta %>%
+#   write_parquet(here("/home/chase/code/hf/barkai_compendium/GSE222268_metadata.parquet"),
+#                 compression = "zstd",
+#                 write_statistics = TRUE,
+#                 use_dictionary = c(
+#                   sample_id = TRUE,
+#                   regulator_locus_tag = TRUE,
+#                   regulator_symbol = TRUE,
+#                   accession = TRUE
+#                 )
+#   )