patchwork.copynumbers: Function plot allele-specific copy numbers of the genome

In xu-chang/patchwork-lite: Allele-specific Copy Number Analysis of whole genome data

Description

Input data for this function should be assessed from any of the karyotype_chroms() plots. For example <yoursample>_karyotype.chr<1-22,X,Y>.png.

See argument details.

Usage

patchwork.copynumbers(CNfile,cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F,male.sample=F,male2femref=F)

Arguments

CNfile	The name and path of your copynumbers file, generated from patchwork.plot(). Example Myfile_copynumbers.Rdata.
cn2	The approximate position of copy number 2,diploid, on total intensity / coverage axis.
delta	The difference in total intensity between consecutive copy numbers. For example 1 and 2 or 2 and 3. If copy number 2 has total intensity ~0.6 and copy number 3 har total intensity ~0.8 then delta would be 0.2.
het	Allelic imbalance ratio of heterozygous copy number 2.
hom	Allelic imbalance ratio of Loss-of-heterozygosity copy number 2.
maxCn	Highest copy number to calculate for. Default is 8.
ceiling	Default is 1.
forcedelta	Default is FALSE. If TRUE the delta value will not be subject to small adjustment changes.
male.sample	Default is FALSE. If it is a male sample put TRUE here and it will handle the XY chromosomes better.
male2femref	Default is FALSE. If TRUE the sample is male but the reference you used is female. This will correct for this.

Details

1. Run the patchwork.plot correctly. This will generate <yourfile>_copynumbers.Rdata. 2. View your plots and decide the correct parameters for the other arguments of this function. 4. Run the function.

Author(s)

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

See Also

patchwork.plot
subfunctions_copynumbers

xu-chang/patchwork-lite documentation built on May 26, 2019, 6:31 a.m.