patchwork.alleledata: patchwork alleledata function

Description Usage Arguments Details Author(s) See Also

View source: R/patchwork.alleledata.r

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

1
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, [email protected] Sebastian DiLorenzo, [email protected]

See Also

patchwork.plot


patchwork documentation built on May 31, 2017, 2:54 a.m.