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add prefix and conf for readGistic function #1102

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add prefix and conf for readGistic function #1102

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20 changes: 11 additions & 9 deletions R/readGistic.R
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Original file line number Diff line number Diff line change
Expand Up @@ -19,19 +19,20 @@
#' @details
#' Requires output files generated from GISTIC. Gistic documentation can be found here ftp://ftp.broadinstitute.org/pub/GISTIC2.0/GISTICDocumentation_standalone.htm

readGistic = function(gisticDir = NULL, gisticAllLesionsFile = NULL, gisticAmpGenesFile = NULL, gisticDelGenesFile = NULL, gisticScoresFile = NULL, cnLevel = 'all', isTCGA = FALSE, verbose = TRUE){
readGistic = function(gisticDir = NULL, gisticAllLesionsFile = NULL, gisticAmpGenesFile = NULL, gisticDelGenesFile = NULL, gisticScoresFile = NULL, cnLevel = 'all', conf=NULL, prefix="", isTCGA = FALSE, verbose = TRUE){

if(!is.null(gisticDir)){
lf = list.files(gisticDir)
lf = lf[startsWith(lf,'all_lesions.conf_')]

#Parse conf interval from all_lesions.conf_99.txt file
conf = gsub(pattern = "[A-Z]|[[:punct:]]", replacement = "", x = basename(lf), ignore.case = TRUE)

gisticAllLesionsFile <- file.path(gisticDir, paste0("all_lesions.conf_",conf,".txt"))
gisticAmpGenesFile <- file.path(gisticDir, paste0("amp_genes.conf_",conf,".txt"))
gisticDelGenesFile <- file.path(gisticDir, paste0("del_genes.conf_",conf,".txt"))
gisticScoresFile <- file.path(gisticDir, "scores.gistic")
if (is.null(conf)){
conf = gsub(pattern = "[A-Z]|[[:punct:]]", replacement = "", x = basename(lf), ignore.case = TRUE)
}
gisticAllLesionsFile <- file.path(gisticDir, paste0(prefix, "all_lesions.conf_",conf,".txt"))
gisticAmpGenesFile <- file.path(gisticDir, paste0(prefix, "amp_genes.conf_",conf,".txt"))
gisticDelGenesFile <- file.path(gisticDir, paste0(prefix, "del_genes.conf_",conf,".txt"))
gisticScoresFile <- file.path(gisticDir, paste0(prefix, "scores.gistic"))

if(!file.exists(gisticAllLesionsFile)){
gisticAllLesionsFile = NULL
Expand Down Expand Up @@ -76,8 +77,9 @@ readGistic = function(gisticDir = NULL, gisticAllLesionsFile = NULL, gisticAmpGe
}

# get 99 from "all_lesions.conf_99.txt", get 95 from "all_lesions.conf_95.txt", etc.
conf = gsub(pattern = "[A-Z]|[[:punct:]]", replacement = "", x = basename(gisticAllLesionsFile), ignore.case = TRUE)

if (is.null(conf)){
conf = gsub(pattern = "[A-Z]|[[:punct:]]", replacement = "", x = basename(gisticAllLesionsFile), ignore.case = TRUE)
}
if(verbose){
cat('-Processing Gistic files..\n')
}
Expand Down