minor drug curations

sigven · May 23, 2024 · 6d17c27 · 6d17c27
1 parent 9260529
commit 6d17c27
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Showing 5 changed files with 15 additions and 11 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pharmOncoX
 Type: Package
 Title: Molecularly targeted cancer drugs and biomarkers
 Version: 1.6.6
-Date: 2024-05-21
+Date: 2024-05-23
 Authors@R: 
     c(person(given = "Sigve",
              family = "Nakken",

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,7 @@
-# Version 1.6.6 (May 21st 2024)
+# Version 1.6.7 (May 23rd 2024)
 
 * NCI update (24.04e)
-* Updated CIViC (20240521)
+* Updated CIViC (20240523)
 
 # Version 1.6.4 (April 30th 2024)
 

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/biomarker_utilities.R b/data-raw/biomarker_utilities.R
@@ -1308,7 +1308,8 @@ load_civic_biomarkers <- function(
       alias_type, "genomic"))
   variants_expanded_mut2$alteration_type <- NULL
   variants_expanded_mut2 <- variants_expanded_mut2 |>
-    dplyr::left_join(variants_nongenomic, by = "variant_id")
+    dplyr::left_join(variants_nongenomic, by = "variant_id",
+                     relationship = "many-to-many")
 
   variants_expanded[['mut']] <- variants_expanded_mut1 |>
     dplyr::bind_rows(variants_expanded_mut2)
@@ -2503,7 +2504,8 @@ load_pmkb_biomarkers <- function(cache_dir = NA) {
     dplyr::filter(alteration_type != "CNA") |>
     dplyr::select(-c(variant, alteration_type, variant_type)) |>
     dplyr::left_join(variants_expanded[['mut']],
-                     by = c("symbol", "evidence_id"), multiple = "all") |>
+                     by = c("symbol", "evidence_id"), 
+                     relationship = "many-to-many") |>
     dplyr::distinct() |>
     dplyr::bind_rows(
       dplyr::filter(pmkb_phenotype_mapped,

diff --git a/data-raw/custom_drug_target_regex_nci.tsv b/data-raw/custom_drug_target_regex_nci.tsv
@@ -2,6 +2,8 @@ pattern	symbol
 OMX-0407	SIK3
 RMC-9085	KRAS
 3706674	KRAS
+Rineterkib	ERK1
+Rineterkib	ERK2
 Zoligratinib	FGFR1
 Zoligratinib	FGFR2
 Zoligratinib	FGFR3
@@ -563,17 +565,17 @@ Aromatase Inhibitor	CYP19A1
 Bexmarilimab	STAB1
 Sonepcizumab	MBTPS1
 Src/tubulin Inhibitor KX2-361	SRC
-Domatinostat|Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor|Zabadinostat	HDAC1
-Domatinostat|Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor|Zabadinostat	HDAC2
-Domatinostat|Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor|Zabadinostat	HDAC3
-Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor	HDAC8
+Domatinostat|Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor|Zabadinostat|Purinostat	HDAC1
+Domatinostat|Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor|Zabadinostat|Purinostat	HDAC2
+Domatinostat|Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor|Zabadinostat|Purinostat	HDAC3
+Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor|Purinostat	HDAC8
 Histone Deacetylase Inhibitor|Class 1/4 Histone Deacetylase Inhibitor	HDAC11
 Givinostat|HDAC Class I/IIb Inhibitor	HDAC1
 Givinostat|HDAC Class I/IIb Inhibitor	HDAC2
 Givinostat|HDAC Class I/IIb Inhibitor	HDAC3
 Givinostat|HDAC Class I/IIb Inhibitor	HDAC8
-Givinostat|HDAC Class I/IIb Inhibitor	HDAC6
-Givinostat|HDAC Class I/IIb Inhibitor|Tucidinostat	HDAC10
+Givinostat|HDAC Class I/IIb Inhibitor|Purinostat	HDAC6
+Givinostat|HDAC Class I/IIb Inhibitor|Tucidinostat|Purinostat	HDAC10
 Quisinostat|Pracinostat|Remetinostat|Resminostat|Tefinostat|Tucidinostat	HDAC1
 Quisinostat|Pracinostat|Remetinostat|Resminostat|Tefinostat|Tucidinostat	HDAC2
 Quisinostat|Pracinostat|Remetinostat|Resminostat|Tefinostat|Tucidinostat	HDAC3