Merge pull request #11 from taylor-lab/legacyoncokb

Legacy oncokb URL replacement
taylor-lab · Nov 11, 2024 · e8af3e0 · e8af3e0
2 parents 2e82ee5 + 52355be
commit e8af3e0
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diff --git a/R/hotspot-annotate-maf.R b/R/hotspot-annotate-maf.R
@@ -18,14 +18,14 @@
 #' @name hotspot_annotate_maf
 NULL
 
-load_gene_annotation = function(oncokbbaseurl = 'https://legacy.oncokb.org/api/v1/genes') {
+load_gene_annotation = function(oncokbbaseurl = 'https://data-legacy.oncokb.aws.mskcc.org/api/v1/genes') {
     read_lines(oncokbbaseurl) %>%
         fromJSON()
 }
 
 #' @export
 #' @rdname hotspot_annotate_maf
-hotspot_annotate_maf = function(maf, oncokbbaseurl = 'https://legacy.oncokb.org/api/v1/genes', hotspot_tbl = NULL) {
+hotspot_annotate_maf = function(maf, oncokbbaseurl = 'https://data-legacy.oncokb.aws.mskcc.org/api/v1/genes', hotspot_tbl = NULL) {
 
     if (!inherits(maf, 'data.frame')) stop('Input MAF must be a data frame, preferrable VEP annotated')
     if (!is.null(hotspot_tbl)) {

diff --git a/R/oncokb-annotate-maf.R b/R/oncokb-annotate-maf.R
@@ -67,7 +67,7 @@ query_oncokb = function(gene, protein_change, variant_type, start, end, cancer_t
 
   if (variant_type != '') {
 
-    base_url = 'http://oncokb.org/legacy-api/indicator.json?source=cbioportal'
+    base_url = 'https://data-legacy.oncokb.aws.mskcc.org/legacy-api/indicator.json?source=cbioportal'
     oncokb_version = httr::content(httr::GET(base_url))[['dataVersion']]
     tag = paste(gene, protein_change, cancer_type, sep = '-')