update_readme_paperlink

README.md

@@ -14,36 +14,9 @@ pretty_name: "Kemmeren, 2014 Overexpression"
 size_categories:
 - 1M<n<10M
 
-experimental_conditions:
-  temperature_celsius: 30
-  cultivation_method: plate
-  growth_phase_at_harvest:
-    phase: "early_mid_log"
-    od600: 0.6
-    od600_tolerance: 0.1
-  media:
-    name: synthetic_complete
-    carbon_source:
-      - compound: D-glucose
-        # Kemmeren et al 2014: 2% D-glucose
-        concentration_percent: 2
-    nitrogen_source:
-      - compound: yeast_nitrogen_base
-        # Kemmeren et al 2014: 6.71 g/l
-        concentration_percent: 0.671
-        specifications:
-          - without_amino_acids
-          - without_carbohydrate
-          - with_ammonium_sulfate
-      - compound: amino_acid_dropout_mix
-        # Kemmeren et al 2014: 2.0 g/l
-        concentration_percent: 0.2
-citation: https://doi.org/10.1016/j.cell.2014.02.054
 configs:
 - config_name: kemmeren_2014
-  description: >-
-    Transcriptional regulator overexpression perturbation data with
-    differential expression measurements
+  description: Transcriptional regulator overexpression perturbation data with differential expression measurements
   dataset_type: annotated_features
   default: true
   metadata_fields: ["regulator_locus_tag", "regulator_symbol"]
@@ -52,183 +25,36 @@ configs:
     path: kemmeren_2014.parquet
   dataset_info:
     features:
-    - name: sample_id
-      dtype: integer
-      description: >-
-        unique identifier for a specific sample.
-        The sample ID identifies a unique regulator.
-    - name: db_id
-      dtype: integer
-      description: >-
-        an old unique identifer, for use internally only. Deprecated and will be removed eventually.
-        Do not use in analysis. db_id = 0 for loci that were originally parsed incorrectly.
     - name: regulator_locus_tag
       dtype: string
-      description: >-
-        induced transcriptional regulator systematic ID.
-        See hf/BrentLab/yeast_genome_resources
+      description: induced transcriptional regulator systematic ID. See hf/BrentLab/yeast_genome_resources
       role: regulator_identifier
     - name: regulator_symbol
       dtype: string
-      description: >-
-        induced transcriptional regulator common name.
-        If no common name exists, then the `regulator_locus_tag` is used.
+      description: induced transcriptional regulator common name. If no common name exists, then the `regulator_locus_tag` is used.
       role: regulator_identifier
     - name: reporterId
       dtype: string
       description: probe ID as reported from the original data
     - name: target_locus_tag
       dtype: string
-      description: >-
-        The systematic ID of the feature to which the effect/pvalue is assigned.
-        See hf/BrentLab/yeast_genome_resources
+      description: The systematic ID of the feature to which the effect/pvalue is assigned. See hf/BrentLab/yeast_genome_resources
       role: target_identifier
     - name: target_symbol
       dtype: string
-      description: >-
-        The common name of the feature to which the effect/pvalue is assigned.
-        If there is no common name, the `target_locus_tag` is used.
+      description: The common name of the feature to which the effect/pvalue is assigned. If there is no common name, the `target_locus_tag` is used.
       role: target_identifier
     - name: M
       dtype: float64
       description: log₂ fold change (mutant vs wildtype)
       role: quantitative_measure
-    - name: Madj
-      dtype: float64
-      description: >-
-        M value with the cell cycle signal removed
-        (see paper cited in the introduction above)
-      role: quantitative_measure
     - name: A
       dtype: float64
-      description: >-
-        average log2 intensity of the two channels, a proxy for expression level
-        (This is a guess based on microarray convention -- not specified on holstege site)
-      role: quantitative_measure
-    - name: pval
-      dtype: float64
-      description: significance of the modeled effect (M), from limma
-      role: quantitative_measure
-    - name: variable_in_wt
-      dtype: string
-      description: >-
-        True if the given locus is variable in the WT condition.
-        Recommended to remove these from analysis. False otherwise.
-        See Holstege website for more information
-      role: experimental_condition
-    - name: multiple_probes
-      dtype: string
-      description: >-
-        True if there is more than one probe associated with
-        the same genomic locus. False otherwise
-      role: experimental_condition
-    - name: kemmeren_regulator
-      dtype: string
-      description: >-
-        True if the regulator is one of the regulators studied in the
-        original Kemmeren et al. (2014) global regulator study. False otherwise
-      role: experimental_condition
-    - name: regulator_desc
-      dtype: string
-      description: >-
-        functional description of the induced regulator
-        from the original paper supplement
-      role: experimental_condition
-    - name: functional_category
-      dtype: string
-      description: functional classification of the regulator from the original paper supplement
-      role: experimental_condition
-    - name: slides
-      dtype: string
-      description: identifier(s) for the microarray slide(s) used in this experiment
-      role: experimental_condition
-    - name: mating_type
-      dtype: string
-      description: mating type of the strain background used in the experiment
-      role: experimental_condition
-    - name: source_of_deletion_mutants
-      dtype: string
-      description: origin of the strain
-      role: experimental_condition
-    - name: primary_hybsets
-      dtype: string
-      description: identifier for the primary hybridization set to which this sample belongs
-      role: experimental_condition
-    - name: responsive_non_responsive
-      dtype: string
-      description: >-
-        classification of the regulator as responsive or not to the
-        deletion from the original paper supplement
-      role: experimental_condition
-    - name: nr_sign_changes
-      dtype: integer
-      description: >-
-        number of significant changes in expression detected for the regulator locus tag (abs(M) > log2(1.7) & pval < 0.05).
-        Note that there is a slight difference when calculating from the data provided here, I believe due to a difference in
-        the way the targets are parsed and filtered (some ORFs that have since been removed from the annotations are removed).
-        I didn't investigate this closely, though.
-      role: experimental_condition
-    - name: profile_first_published
-      dtype: string
-      description: citation or reference indicating where this expression profile was first published
-      role: experimental_condition
-    - name: chase_notes
-      dtype: string
-      description: notes added during data curation and parsing
-    - name: responsive
-      dtype: string
-      description: Per the paper(s), The authors consider a target responsive if Madj > 1.7 and pval < 0.05
-
-- config_name: control_2014
-  description: This stores the WT/background strains "WT-BY4743", "WT-MATA" and "WT-YPD" from Kemmeren 2014
-  dataset_type: annotated_features
-  metadata_fields: ["strain"]
-  data_files:
-  - split: train
-    path: control_2014.parquet
-  dataset_info:
-    features:
-    - name: sample_id
-      dtype: integer
-      description: >-
-        unique identifier for a specific sample.
-        The sample ID identifies a unique regulator.
-    - name: strain
-      dtype: string
-      description: >-
-        The genotype or strain used in the experiment,
-        one of "WT-BY4743", "WT-MATA" and "WT-YPD"
-      role: regulator_identifier
-    - name: regulator_symbol
-      dtype: string
-      description: >-
-        induced transcriptional regulator common name.
-        If no common name exists, then the `regulator_locus_tag` is used.
-      role: regulator_identifier
-    - name: reporterId
-      dtype: string
-      description: probe ID as reported from the original data
-    - name: target_locus_tag
-      dtype: string
-      description: >-
-        The systematic ID of the feature to which the effect/pvalue is assigned.
-        See hf/BrentLab/yeast_genome_resources
-      role: target_identifier
-    - name: target_symbol
-      dtype: string
-      description: >-
-        The common name of the feature to which the effect/pvalue is assigned.
-        If there is no common name, the `target_locus_tag` is used.
-      role: target_identifier
-    - name: M
-      dtype: float64
-      description: log₂ fold change (mutant vs wildtype)
+      description: average log₂ intensity of the two channels, a proxy for expression level (This is a guess based on microarray convention -- not specified on holstege site)
       role: quantitative_measure
-    - name: A
+    - name: Madj
       dtype: float64
-      description: >-
-        average log2 intensity of the two channels, a proxy for expression level
-        (This is a guess based on microarray convention -- not specified on holstege site)
+      description: M value with the cell cycle signal removed (see paper cited in the introduction above)
       role: quantitative_measure
     - name: pval
       dtype: float64
@@ -236,41 +62,12 @@ configs:
       role: quantitative_measure
     - name: variable_in_wt
       dtype: string
-      description: >-
-        True if the given locus is variable in the WT condition.
-        Recommended to remove these from analysis. False otherwise.
-        See Holstege website for more information
+      description: True if the given locus is variable in the WT condition. Recommended to remove these from analysis. False otherwise. See Holstege website for more information
       role: experimental_condition
     - name: multiple_probes
       dtype: string
-      description: >-
-        True if there is more than one probe associated with
-        the same genomic locus. False otherwise
+      description: True if there is more than one probe associated with the same genomic locus. False otherwise
       role: experimental_condition
-    - name: kemmeren_regulator
-      dtype: string
-      description: >-
-        True if the regulator is one of the regulators studied in the
-        original Kemmeren et al. (2014) global regulator study. False otherwise
-      role: experimental_condition
-    - name: description
-      dtype: string
-      description: >-
-        functional description of the induced regulator
-        from the original paper supplement
-      role: experimental_condition
-    - name: mating_type
-      dtype: string
-      description: mating type of the strain background used in the experiment
-      role: experimental_condition
-    - name: chase_notes
-      dtype: string
-      description: notes added during data curation and parsing
-    - name: responsive
-      dtype: string
-      description: >-
-        Per the paper(s), The authors consider a target responsive
-        if M > 1.7 and pval < 0.05
 ---
 # Kemmeren 2014
 

control_2014.parquet

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:490665c992e5c586a914077e10578bec0a829f54425a1212b40021f174926133
-size 661123

kemmeren_2014.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:e4003f0d49e17671ccf29f39e36b0e95091aba7988b3d3f6b371f2ecd1a4930f
-size 301348699
+oid sha256:3c463017444bd7690959c0d6fff0d0ebe2faa7b916dd9c44e305156f6c98b863
+size 319218929

kemmeren_2014.parquet.md5

@@ -0,0 +1 @@
+9109e2e853acab9fa341a1eebc1c649c  kemmeren_2014.parquet

scripts/parse_kemmeren_data.R

@@ -119,14 +119,9 @@ deleteome_all_mutants_controls_long = deleteome_all_mutants_controls %>%
   mutate(kemmeren_regulator = toupper(str_remove(tolower(kemmeren_regulator), "-del-1$|-del-mata$|-del$"))) %>%
   mutate(kemmeren_regulator = ifelse(kemmeren_regulator == "ARG5,6", "ARG56", kemmeren_regulator))
 
-kem_sup1_regulator_info = read_excel(here("data/kemmeren/supplemental_table1_strain_info.xlsx")) %>%
-  mutate(`profile first published` = str_replace(`profile first published`, ", ", ","))
-kem_sup1_regulator_info_straininfo = read_excel(here("data/kemmeren/supplemental_table1_strain_info_origins.xlsx"))
-
-kem_sup1_regulator_info = kem_sup1_regulator_info %>%
-  left_join(kem_sup1_regulator_info_straininfo) %>%
-  mutate(`profile first published` = citation) %>%
-  select(-citation)
+kem_sup1_regulator_info = read_excel(here("data/kemmeren/mmc1.xlsx")) %>%
+  # additional columns are not tabular
+  .[,1:9]
 
 parsed_regulators = deleteome_all_mutants_controls_long %>%
   select(kemmeren_regulator) %>%
@@ -184,8 +179,7 @@ regulators_munging_df = bind_rows(regulators_munging_list) %>%
                     regulator_symbol = symbol)) %>%
   replace_na(list(chase_notes = "none")) %>%
   mutate(regulator_locus_tag = ifelse(str_detect(kemmeren_regulator, "^WT-"), kemmeren_regulator, regulator_locus_tag),
-         regulator_symbol = ifelse(str_detect(kemmeren_regulator, "^WT-"), kemmeren_regulator, regulator_symbol)) %>%
-  janitor::clean_names()
+         regulator_symbol = ifelse(str_detect(kemmeren_regulator, "^WT-"), kemmeren_regulator, regulator_symbol))
 
 
 stopifnot(setequal(regulators_munging_df$kemmeren_regulator,
@@ -257,48 +251,20 @@ final_parsed_df = Reduce(left_join, final_parsed_list) %>%
   # duplicated to mulitple Madj. This removes those duplicates
   distinct(reporterId, .keep_all = TRUE) %>%
   ungroup() %>%
-  left_join(select(regulators_munging_df,
-                   -c(gene, `orf_name`))) %>%
-  dplyr::rename(nr_sign_changes = nr_sign_changes_p_0_05_fc_1_7,
-                primary_hybsets = primary_hybset_s,
-                source_of_deletion_mutants = source_of_deletion_mutant_s,
-                slides = slide_s,
-                regulator_desc = description) %>%
-  arrange(regulator_locus_tag)
-  # select(regulator_locus_tag, regulator_symbol, reporterId,
-  #        target_locus_tag, target_symbol, M, Madj, A, pval,
-  #        variable_in_wt, multiple_probes)
-
-db_kemmeren_meta = read_csv("data/kemmeren/db_kemmeren_meta_20251126.csv") %>%
-  mutate(id = ifelse(regulator_locus_tag == 'YLR352W', 0, id)) %>%
-  select(id, regulator_locus_tag) %>%
-  distinct() %>%
-  mutate(id = as.integer(id)) %>%
-  dplyr::rename(db_id = id)
+  left_join(select(regulators_munging_df, kemmeren_regulator,
+                   regulator_locus_tag, regulator_symbol)) %>%
+  select(regulator_locus_tag, regulator_symbol, reporterId,
+         target_locus_tag, target_symbol, M, Madj, A, pval,
+         variable_in_wt, multiple_probes)
 
-final_df_parsed_with_ids = final_parsed_df %>%
-  left_join(db_kemmeren_meta) %>%
-  replace_na(list(db_id = 0)) %>%
+final_parsed_df %>%
   arrange(regulator_locus_tag) %>%
-  group_by(regulator_locus_tag) %>%
-  mutate(sample_id = cur_group_id()) %>%
-  relocate(sample_id, db_id,
-           regulator_locus_tag, regulator_symbol,
-           reporterId, target_locus_tag, target_symbol,
-           M, Madj, A, pval,
-           variable_in_wt, multiple_probes)
-
-# note! verify before overwriting that the sample_id for the unique sample
-# tuple is the same as it is in the current hackett_2020, or that any changes
-# are intentional
-
-# final_df_parsed_with_ids %>%
-#   write_parquet("~/code/hf/kemmeren_2014/kemmeren_2014.parquet",
-#                 compression = "zstd",
-#                 chunk_size = 6181,
-#                 write_statistics = TRUE,
-#                 use_dictionary = c(
-#                   regulator_locus_tag = TRUE,
-#                   target_locus_tag = TRUE
-#                 )
-#   )
+  write_parquet(here("data/kemmeren/kemmeren_2014.parquet"),
+                compression = "zstd",
+                chunk_size = 6181,
+                write_statistics = TRUE,
+                use_dictionary = c(
+                  regulator_locus_tag = TRUE,
+                  target_locus_tag = TRUE
+                )
+  )