extractXvarlinkData: Extract Data From XVarLink Fields

In dami82/mutSignatures_dev: Decipher Mutational Signatures from Somatic Mutational Catalogs

Usage

extractXvarlinkData(xvarLink_data)

Arguments

xvarLink_data

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (xvarLink_data) 
{
    tmpVars <- sub("^.*&var=[[:alnum:]]+(,.*)&.*$", "\1", xvarLink_data)
    tmpVars[!grepl("^,.+", tmpVars)] <- NA
    tmpVars <- strsplit(tmpVars, ",")
    tmpVars <- do.call(rbind, lapply(1:length(tmpVars), function(i) {
        if (tmpVars[[i]][1] == "" & length(tmpVars[[i]]) == 5) {
            tmpVars[[i]][2:5]
        }
        else {
            c(NA, NA, NA, NA)
        }
    }))
    out <- data.frame(chrXvar = as.character(tmpVars[, 1]), posXvar = as.numeric(tmpVars[, 
        2]), refXvar = as.character(tmpVars[, 3]), mutXvar = as.character(tmpVars[, 
        4]), stringsAsFactors = FALSE)
    return(out)
  }

dami82/mutSignatures_dev documentation built on May 17, 2019, 7:02 p.m.