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Allow mapWig & repTimeWig to be optional #15

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merged 2 commits into from
Oct 5, 2023
Merged

Allow mapWig & repTimeWig to be optional #15

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e7d30fe
Fix error on optional wig params
ycl6 Sep 20, 2023
549c487
Improve error messaging on required wig params
ycl6 Sep 20, 2023
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17 changes: 14 additions & 3 deletions R/runIchorCNA.R
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Original file line number Diff line number Diff line change
Expand Up @@ -47,8 +47,9 @@
#' @param outDir Output Directory.
#' @param cores Number of cores to use for EM.
#' @export
run_ichorCNA <- function(tumor_wig, normal_wig = NULL, gcWig, mapWig, repTimeWig, normal_panel=NULL, sex = NULL, exons.bed=NULL, id = "test",
centromere = NULL, minMapScore = 0.9, flankLength = 1e5, normal=0.5, estimatePloidy = TRUE, maxFracCNASubclone = 0.7,
run_ichorCNA <- function(tumor_wig, normal_wig = NULL, gcWig, mapWig = NULL, repTimeWig = NULL,
normal_panel = NULL, sex = NULL, exons.bed = NULL, id = "test", centromere = NULL,
minMapScore = 0.9, flankLength = 1e5, normal=0.5, estimatePloidy = TRUE, maxFracCNASubclone = 0.7,
normal.init = "c(0.5, 0.5)", scStates = NULL, scPenalty = 0.1, normal2IgnoreSC = 1.0,
coverage = NULL, likModel = "t", lambda = NULL, lambdaScaleHyperParam = 3,
kappa = 50, ploidy = "2", maxCN = 7, estimateNormal = TRUE, estimateScPrevalence = TRUE,
Expand Down Expand Up @@ -90,7 +91,16 @@ run_ichorCNA <- function(tumor_wig, normal_wig = NULL, gcWig, mapWig, repTimeWig

## load seqinfo
seqinfo <- getSeqInfo(genomeBuild, genomeStyle, chrs)


## check required tumor_wig & gcWig have inputs
if (missing(tumor_wig) || is.null(tumor_wig)) {
stop("tumor wig file not provided but is required")
}

if (missing(gcWig) || is.null(gcWig)) {
stop("GC wig file not provided but is required")
}

if (substr(tumor_wig,nchar(tumor_wig)-2,nchar(tumor_wig)) == "wig") {
wigFiles <- data.frame(cbind(id, tumor_wig))
} else {
Expand Down Expand Up @@ -119,6 +129,7 @@ run_ichorCNA <- function(tumor_wig, normal_wig = NULL, gcWig, mapWig, repTimeWig

## LOAD GC/MAP/REPTIME WIG FILES ###
message("Reading GC and mappability files")

gc <- wigToGRanges(gcWig)
if (is.null(gc)){
stop("GC wig file not provided but is required")
Expand Down
2 changes: 2 additions & 0 deletions R/utils.R
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Expand Up @@ -93,6 +93,8 @@ setGenomeStyle <- function(x, genomeStyle = "NCBI", species = "Homo_sapiens"){
}
#' @export
wigToGRanges <- function(wigfile, verbose = TRUE){
if(is.null(wigfile)) return(NULL)

output <- tryCatch({
input <- readLines(wigfile, warn = FALSE)
breaks <- c(grep("fixedStep", input), length(input) + 1)
Expand Down