read.illumina: Illustrative function to an Illumina GenomeStudio file.

In jjellis/GenomicVis: Genomic Visualisation Routines

Description

This function is an example of reading the output of GenomeStudio and producing a data.frame required by cnv.plot.

Usage

read.illumina(file, snp.name = "SNP Name", sample.name = "Sample ID",
  chr.name = "Chr", pos.name = "Position", baf.name = "B Allele Freq",
  lrr.name = "Log R Ratio")

Arguments

file	The GenomeStudio file to process.
snp.name	The name of the SNP ID column.
sample.name	The name of the sample ID column.
chr.name	The name of the chromosome column.
pos.name	The name of the SNP position column.
baf.name	The name of the B allele frequency column.
lrr.name	The name of the log R ratio column.

Details

The input file is the output (i.e., final report) from GenomeStudio. It must contain at least six columns with the SNP name, sample ID, chromosome, position B allele frequency and log R ratio in it. The exact column name must match the parameters chr.name, pos.name, baf.name and lrr.name respectively.

Value

A data.table instance with six columns: SNP.Name, Sample.ID, Chr, Position, BAF and LRR.

Author(s)

Jonathan Ellis <[e-mail]>

Examples

## Not run: 
x <- read.illumina('LC1_TUMOUR_A_FinalReport.txt')

## End(Not run)

jjellis/GenomicVis documentation built on May 19, 2019, 11:39 a.m.