readCNVs: Given a filename of a TCGA cnv file opens and convert it to...
In NilsWeng/TCGAproject_repo: What the package does (short line)

Description Usage Arguments Examples

Given a filename of a TCGA cnv file opens and convert it to GRanges object

1	readCNVs(filename)

filename

##---- 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 (filename) 
{
    suppressPackageStartupMessages(library("GenomicRanges"))
    cnv_DF <- read.table(filename, header = TRUE, sep = "\t", 
        stringsAsFactors = FALSE)
    cnv_GRanges <- GRanges(seqnames = cnv_DF$Chromosome, ranges = IRanges(cnv_DF$Start, 
        cnv_DF$End), strand = "*", Num_Probes = cnv_DF$Num_Probes, 
        Segment_Mean = cnv_DF$Segment_Mean,
        GDC_Aliquot = cnv_DF$GDC_Aliquot)
        
    return(cnv_GRanges)
  }