#' Load the quality control files (.qc) generated by OncoSNP.
#'
#' @param qcFile File generated that can be generated in the oncosnp module or
#' a single qc file generated by oncosnp directly.
#' @return A data.frame of the quality control file that has its columns
#' renamed to be programmer-friendly to use.
#' @export
load_oncosnp_qc_file <- function(qcFile) {
inDt <- data.table::fread(qcFile)
data.table::setnames(inDt,
colnames(inDt),
c("LRRShift", "normalContent", "copyNum",
"logLikelihood", "outlierRate",
"LRRStd", "BAFStd", "ploidyNo"))
return(dplyr::tbl_df(inDt))
}
#' Load the OncoSNP CNV file (.cnv).
#'
#' @param cnvFile OncoSNP CNV file
#' @return A data.table of the standard output file (.cnvs) that has its columns
#' renamed to be programmer-friendly to use
#' @export
load_oncosnp_cnv_file <- function(cnvFile, version = c("1.3.0")) {
cnvDt <- data.table::fread(cnvFile)
# if (version == "1.2"){
# colnames(inDf)[1:3] <- c('chr', 'start', 'end')
# colnames(inDf)[7] <- 'num.markers'
# colnames(inDf)[10] <- 'state'
if (numeric_version(version) == numeric_version("1.3.0")){
data.table::setnames(cnvDt,
colnames(cnvDt),
c("chr", "start", "end", "copyNum", "loh", "rank",
"logLik", "numMarkers", "normFrac", "state",
"ploidyNum", "majorCopyNumber", "minorCopyNumber")
)
}
return(dplyr::tbl_df(cnvDt))
}
#' Load the PennCNV probe data.
#'
#' @param probeFile The PennCNV probe file
#' @return A data.table of the probe file
#' @export
load_penncnv_probe_data <- function(probeFile){
probeDt <- data.table::fread(probeFile, colClasses = c("Chr" = "character"))
data.table::setnames(probeDt,
colnames(probeDt),
c("probeID", "chr", "pos", "LRR", "BAF"))
return(dplyr::tbl_df(probeDt))
}
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