move analysis C (annotation for manual review)

halbritter-lab · Oct 11, 2023 · babcf37 · babcf37
1 parent 5912f11
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Showing 7 changed files with 231 additions and 111 deletions.
diff --git a/analyses/AnnotateMergedTable.R → ...notateMergedTable/C_AnnotateMergedTable.R b/analyses/AnnotateMergedTable.R → ...notateMergedTable/C_AnnotateMergedTable.R
diff --git a/analyses/C_AnnotateMergedTable/results/C_high_evidence_annotated_csv_table.2023-10-11.csv.gz b/analyses/C_AnnotateMergedTable/results/C_high_evidence_annotated_csv_table.2023-10-11.csv.gz
diff --git a/...tateMergedTable/results/merge_analyses_sources_high_evidence_expression.2023-10-11.csv.gz b/...tateMergedTable/results/merge_analyses_sources_high_evidence_expression.2023-10-11.csv.gz
diff --git a/.../C_AnnotateMergedTable/results/merge_analyses_sources_high_evidence_mgi.2023-10-11.csv.gz b/.../C_AnnotateMergedTable/results/merge_analyses_sources_high_evidence_mgi.2023-10-11.csv.gz
diff --git a/...AnnotateMergedTable/results/merge_analyses_sources_high_evidence_string.2023-10-11.csv.gz b/...AnnotateMergedTable/results/merge_analyses_sources_high_evidence_string.2023-10-11.csv.gz
diff --git a/analyses/C_AnnotateMergedTable/stringdb_protein_links.2023-10-11.txt.gz b/analyses/C_AnnotateMergedTable/stringdb_protein_links.2023-10-11.txt.gz
diff --git a/analyses/functions/gtex-functions.R b/analyses/functions/gtex-functions.R
@@ -79,6 +79,8 @@ get_median_tissue_expression <- function(gencode_ids, tissue_site_detail_ids = N
 }
 
 
+# TODO: fix the gtex function get_multiple_median_tissue_expression to work properly with multiple gencode ids instead of using rowwise
+# TODO: fix the gtex functions to implement retry logic if the API call results in an error or empty result
 #' Fetch Median Tissue Expression Levels from GTEx API for Multiple Genes
 #'
 #' This function takes a character vector of GENCODE gene identifiers as input,