normalizeMirroredBAFsByRegions.matrix: Normalizes region-level mirrored allele B fractions (mBAFs)

In HenrikBengtsson/aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

Normalizes region-level mirrored allele B fractions (mBAFs)

Description

Normalizes region-level mirrored allele B fractions (mBAFs) for heterozygous and homozygous SNPs by rescaling both equally much such that the normalized homozygous mBAFs become exactly or close to their expected values (which is at zero and one).

Usage

## S3 method for class 'matrix'
normalizeMirroredBAFsByRegions(data, flavor=c("plain", "total"), ..., verbose=FALSE)

Arguments

data	A numeric Kx2 or Kx3 matrix, where K is the number of segments and the first and the second column contains average heterozygous and homozygous mBAF estimates, respectively. The third column, which is optional, contains total copy numbers.
flavor	A character string specifying how the normalization function/scale factors are estimated.
...	Additional arguments passed fitXYCurve, which is used if flavor="total".
verbose	See Verbose.

Details

The mBAFs for heterozygous SNPs are also known as the Decrease in Heterozygosity signals (DHs).

Value

A numeric matrix of the same dimensions as argument data.

Author(s)

Henrik Bengtsson, Pierre Neuvial

HenrikBengtsson/aroma.cn documentation built on Feb. 20, 2024, 9:15 p.m.