From 10edf55929f51cf5239938368220268eeea37fdc Mon Sep 17 00:00:00 2001 From: skchronicles Date: Tue, 3 Sep 2019 15:19:12 -0400 Subject: [PATCH] Adding support for hg38_30 to karyoploter.R --- Results-template/Scripts/karyoploter.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Results-template/Scripts/karyoploter.R b/Results-template/Scripts/karyoploter.R index 0eccfe3..30fc09e 100644 --- a/Results-template/Scripts/karyoploter.R +++ b/Results-template/Scripts/karyoploter.R @@ -6,7 +6,7 @@ parser$add_argument("-d", "--degout", type="character", required=TRUE, parser$add_argument("-c", "--gene2coord", type="character", required=TRUE, help="Gene to coordinate file") parser$add_argument("-g", "--genome", type="character", required=TRUE, - help="Genome .. either hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3") + help="Genome .. either hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3/hg38_30") parser$add_argument("-f", "--fdr", type="double", default=0.05, help="FDR cutoff to use") parser$add_argument("-o", "--outfileprefix", type="character", required=TRUE, @@ -20,8 +20,8 @@ if (! file.exists(f)) { stop(paste("File does not exist:",f)) } -if (! args$genome %in% c("hg19","hg38","mm9","mm10","Mmul8.0.1","canFam3")) { - stop("Only hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3 genomes are supported!") +if (! args$genome %in% c("hg19","hg38","hg38_30","mm9","mm10","Mmul8.0.1","canFam3")) { + stop("Only hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3/hg38_30 genomes are supported!") } @@ -54,7 +54,7 @@ if(nrow(deseqout_filtered_w_coord)==0){ genome=args$genome chrs=c() maxchrs=0 -if (genome %in% c("hg19","hg38")) {maxchrs=22} +if (genome %in% c("hg19","hg38","hg38_30")) {maxchrs=22} if (genome %in% c("mm10","mm9")) {maxchrs=19} if (genome %in% c("rheMac8")) {maxchrs=20} if (genome %in% c("canFam3")) {maxchrs=38}