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scripts/parse_hughes_2006.R

@@ -225,6 +225,7 @@ genome_map = tibble(
 stopifnot(setequal(genome_map$hughes_target, unique(df_oe$hughes_target)))
 
 hughes_2006_meta_with_id = hughes_2006_meta %>%
+  arrange(regulator_locus_tag) %>%
   group_by(regulator_locus_tag) %>%
   mutate(sample_id = cur_group_id()) %>%
   ungroup() %>%
@@ -245,20 +246,21 @@ df_oe_harmonized = df_oe %>%
   select(sample_id,
          regulator_locus_tag, regulator_symbol,
          target_locus_tag, target_symbol,
-         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(
-#                   sample_id = TRUE,
-#                   regulator_locus_tag = TRUE,
-#                   regulator_symbol = TRUE,
-#                   target_locus_tag = TRUE,
-#                   target_symbol = TRUE
-#                 )
-#   )
+         dye_plus, dye_minus, mean_norm_log2fc) %>%
+  arrange(sample_id, target_locus_tag)
+
+df_oe_harmonized %>%
+  write_parquet("~/code/hf/hughes_2006/overexpression.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
+                )
+  )
 
 df_ko_harmonized = df_ko %>%
   left_join(
@@ -270,31 +272,32 @@ df_ko_harmonized = df_ko %>%
   select(sample_id,
          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(
-#                   sample_id = TRUE,
-#                   regulator_locus_tag = TRUE,
-#                   regulator_symbol = TRUE,
-#                   target_locus_tag = TRUE,
-#                   target_symbol = TRUE
-#                 )
-#   )
-
-# hughes_2006_meta_with_id %>%
-#   janitor::clean_names() %>%
-#   write_parquet("~/code/hf/hughes_2006/metadata.parquet",
-#                 compression = "zstd",
-#                 write_statistics = TRUE,
-#                 use_dictionary = c(
-#                   sample_id = TRUE,
-#                   regulator_locus_tag = TRUE,
-#                   regulator_symbol = TRUE,
-#                   oe_passed_qc = TRUE,
-#                   del_passed_qc = TRUE
-#                 )
-#   )
+         dye_plus, dye_minus, mean_norm_log2fc) %>%
+  arrange(sample_id, target_locus_tag)
+
+df_ko_harmonized %>%
+  write_parquet("~/code/hf/hughes_2006/knockout.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
+                )
+  )
+
+hughes_2006_meta_with_id %>%
+  janitor::clean_names() %>%
+  write_parquet("~/code/hf/hughes_2006/metadata.parquet",
+                compression = "zstd",
+                write_statistics = TRUE,
+                use_dictionary = c(
+                  sample_id = TRUE,
+                  regulator_locus_tag = TRUE,
+                  regulator_symbol = TRUE,
+                  oe_passed_qc = TRUE,
+                  del_passed_qc = TRUE
+                )
+  )