patchwork.alleledata: patchwork alleledata function

In patchwork: Allele-specific Copy Number Analysis of whole genome data

Description

Loads the data object commonSnps132.RData and uses the perl script, included in package, pile2alleles.pl to generate pile.alleles in your working directory. This will be read into R as the alf object and then the file pile.alleles removed.

Usage

patchwork.alleledata(Pileup,normalalf=NULL,vcf)

Arguments

Pileup	Pileup file from patchwork.plot() input.
normalalf	normalalf is generated and used if you have supplied a normal.pileup in it's argument at patchwork.plot.
vcf	The vcf file if you have used a newer version (>=0.1.17) of SAMtools instead of an older version (<=0.1.16). See patchwork homepage for clarification or just ?patchwork.plot.

Details

Uses SNP data to calculate allele frequencies of the sample. Currently uses SNP132.

patchwork.alleledata is a subfunction to patchwork.plot.

Author(s)

Markus Mayrhofer, [e-mail] Sebastian DiLorenzo, [e-mail]

See Also

patchwork.plot

patchwork documentation built on May 2, 2019, 5:02 p.m.