variant primary name

DESCRIPTION

@@ -2,7 +2,7 @@ Package: pharmOncoX
 Type: Package
 Title: Molecularly targeted cancer drugs and biomarkers
 Version: 1.5.5
-Date: 2024-01-30
+Date: 2024-01-31
 Authors@R: 
  c(person(given = "Sigve",
  family = "Nakken",

NEWS.md

@@ -1,9 +1,10 @@
-# Version 1.5.5 (January 30th 2024)
+# Version 1.5.6 (January 31st 2024)
 
 * Refine possible values in `treatment_category` argument to `get_drugs()` function
 * Fix anti-androgen classification
 * Fixed bug in alias type notation for copy numbers and expression biomarkers
 * Filter noise and rank output in helper function `get_targeted_drugs`
+* Include variant primary name in biomarker variants
 
 # Version 1.5.0 (January 25th 2024)
 

data-raw/biomarker_utilities.R

@@ -430,7 +430,7 @@ expand_hgvs_terms <- function(var, aa_dict, add_codon_markers = FALSE) {
 }
 
 load_civic_biomarkers <- function(
- datestamp = '20240114',
+ datestamp = '20240130',
  compound_synonyms = NULL,
  hg38_fasta = 
  "/Users/sigven/research/DB/hg38/hg38.fa",
@@ -966,7 +966,38 @@ load_civic_biomarkers <- function(
 
  ) |>
  dplyr::distinct()
- )
+ ) |>
+ dplyr::mutate(
+ variant_name_primary = dplyr::case_when(
+ alteration_type == "CNA" |
+ (alteration_type == "MUT_LOF" & !endsWith(variant,"X")) |
+ alteration_type == "METHYL" |
+ stringr::str_detect(
+ variant,
+ "MUTATION|COPY NUMBER VARIATION|TRUNCATING|WILDTYPE|SPLICE SITE|DELETION|AMPLIFICATION") |
+ stringr::str_detect(alteration_type,"^EXP") ~
+ paste0(gene2," ",stringr::str_to_title(variant)),
+ variant_consequence == "transcript_fusion" |
+ (nchar(variant_consequence) == 0 & variant == "FUSION") ~
+ paste0(gene2, " Fusion"),
+ variant == "REARRANGEMENT" ~ 
+ paste0(gene2, " Rearrangement"),
+ TRUE ~ as.character(
+ paste0(gene2, " ", variant)
+ ))
+ ) |>
+ dplyr::mutate(variant_name_primary = stringr::str_replace(
+ variant_name_primary, "FS","fs")
+ ) |>
+ dplyr::mutate(variant_name_primary = stringr::str_replace(
+ variant_name_primary, "DELINS","delins")
+ ) |>
+ dplyr::mutate(variant_name_primary = stringr::str_replace(
+ variant_name_primary, "DEL","del")
+ ) |>
+ dplyr::mutate(variant_name_primary = stringr::str_replace(
+ variant_name_primary, "INS$","ins")
+ )
 
  variants_expanded <- list()
  variants_expanded[['mut']] <- data.frame()
@@ -979,6 +1010,7 @@ load_civic_biomarkers <- function(
  gene <- unique(vrows$gene2)
  variant_consequence <- unique(vrows$variant_consequence)
  alteration_type <- unique(vrows$alteration_type)
+ variant_name_primary <- unique(vrows$variant_name_primary)
 
  all_aliases <- c()
 
@@ -997,6 +1029,7 @@ load_civic_biomarkers <- function(
  df <- data.frame(
  'variant_id' = i,
  'symbol' = gene,
+ 'variant_name_primary' = variant_name_primary,
  'variant_alias' = variant_alias,
  'alteration_type' = alteration_type,
  'variant_consequence' = variant_consequence,
@@ -1284,7 +1317,7 @@ load_civic_biomarkers <- function(
  variantSummary |>
  dplyr::filter(!stringr::str_detect(alteration_type,"MUT")) |>
  dplyr::select(variant_id, variant, variant_consequence,
- variant_alias, alteration_type,
+ variant_alias, variant_name_primary, alteration_type,
  gene2) |>
  dplyr::mutate(variant_alias = dplyr::if_else(
  nchar(variant_alias) > 0,
@@ -1444,6 +1477,7 @@ load_civic_biomarkers <- function(
  biomarker_source_datestamp,
  variant_id,
  variant_alias,
+ variant_name_primary,
  alteration_type,
  alias_type,
  variant_consequence,
@@ -1809,7 +1843,8 @@ load_cgi_biomarkers <- function(compound_synonyms = NULL,
  alteration_type, variant_consequence) |>
  dplyr::arrange(symbol, alteration_type, variant_alias) |>
  dplyr::distinct() |>
- dplyr::mutate(variant_id = dplyr::row_number())
+ dplyr::mutate(variant_id = dplyr::row_number()) |>
+ dplyr::mutate(variant_name_primary = paste(symbol, variant_alias))
  )
 
  cgi_variants <- data.frame()
@@ -1822,6 +1857,7 @@ load_cgi_biomarkers <- function(compound_synonyms = NULL,
  'variant_id' = 
  unique_variants[i,"variant_id"],
  'variant_alias' = t,
+ 'variant_name_primary' = unique_variants[i,"variant_name_primary"],
  'gene' = unique_variants[i,"gene"],
  'entrezgene' = unique_variants[i,"entrezgene"],
  'symbol' = unique_variants[i,"symbol"],
@@ -1858,6 +1894,7 @@ load_cgi_biomarkers <- function(compound_synonyms = NULL,
  biomarker_source_datestamp,
  variant_id,
  variant_alias,
+ variant_name_primary,
  alteration_type,
  alias_type,
  variant_consequence,