readCNVs: Given a filename of a TCGA cnv file opens and convert it to...

Description Usage Arguments Examples

Description

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

Usage

1
readCNVs(filename)

Arguments

filename

Examples

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##---- 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)
  }

NilsWeng/TCGAproject_repo documentation built on May 14, 2019, 4:07 a.m.