From 6975f57cb21f50d173259c9dc63fe72e813cc537 Mon Sep 17 00:00:00 2001 From: sigven Date: Wed, 15 Nov 2017 16:17:13 +0100 Subject: [PATCH] lack of Consequence bug --- src/R/pcgrr/R/utils.R | 4 ++-- src/pcgr.tgz | Bin 24459 -> 24459 bytes 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/R/pcgrr/R/utils.R b/src/R/pcgrr/R/utils.R index 59302673..2c1d61ef 100644 --- a/src/R/pcgrr/R/utils.R +++ b/src/R/pcgrr/R/utils.R @@ -1350,8 +1350,8 @@ get_calls <- function(vcf_gz_file, pcgr_data, sample_id = NULL, tumor_dp_tag = ' vcf_data_df[!is.na(vcf_data_df$PROTEIN_CHANGE) & stringr::str_detect(vcf_data_df$PROTEIN_CHANGE,"^ENSP"),]$PROTEIN_CHANGE <- NA } vcf_data_df$CODING_STATUS <- 'noncoding' - if(nrow(vcf_data_df[stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]) > 0){ - vcf_data_df[stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]$CODING_STATUS <- 'coding' + if(nrow(vcf_data_df[!is.na(vcf_data_df$CONSEQUENCE) & stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]) > 0){ + vcf_data_df[!is.na(vcf_data_df$CONSEQUENCE) & stringr::str_detect(vcf_data_df$CONSEQUENCE,"^(stop_gained|stop_lost|start_lost|frameshift_variant|missense_variant|splice_donor|splice_acceptor|inframe_deletion|inframe_insertion)"),]$CODING_STATUS <- 'coding' } for(col in c('width','strand','totalDepth','refDepth','altDepth','sampleNames')){ diff --git a/src/pcgr.tgz b/src/pcgr.tgz index 3f2bb0038698bada6252c92d6d12eafa2e0954be..a9f78c918dfe7e111c5b51190f3ab3b3227ad5de 100644 GIT binary patch delta 17 YcmeC)&)B`6kxjmvgW*8fMz+>?05_}#00000 delta 17 YcmeC)&)B`6kxjmvgTdWpBU@`c05p6BbpQYW