subfunctions_copynumbers: A number of subfunctions used within patchwork.copynumbers().

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

Description

A number of subfunctions used within patchwork.copynumbers(). These functions are identical in patchworkCG package, so should that package be installed before patchwork or vice versa you will get a non-consequential message saying:

The following object(s) are masked from 'package:patchworkCG':

chrom_ucsc, deChrom_ucsc, is.autosome, weightedMean, weightedMedian

Usage

weightedMedian(data,weights)
weightedMean(data,weights)
is.autosome(vector)
deChrom_ucsc(data)
chrom_ucsc(data)
assignAI(snp_chr,snp_pos,snp_min,snp_max,seg_chr,seg_start,seg_end)

Arguments

data	Object to be handled by the internal function.
weights	Weights to be applied.
vector	The segs objects chr column.
snp_chr	Chromosome.
snp_pos	Position.
snp_min	Lesser allele amount in single position.
snp_max	Greater allele amount in single position.
seg_chr	Segments chromosome.
seg_start	Start position of segment.
seg_end	End position of segment.

Author(s)

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

See Also

patchwork.copynumbers

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