sweepMode: Sweep the modal log R ratio (by row or column) from a matrix...

In VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

Description

This function simplifies the process of sweeping the modal log R ratio from the rows or columns of a SnpArrayExperiment object. It is most useful when a large number of samples (more than 10) are available and the dataset is a collection of germline samples. We assume that the samples are from a single batch and that the modal value will be a robust estimate of the mean log R ratio for diploid copy number. Variation in the modal estimates between markers is presumed to be attributable to probe effects (e.g., differences hybridization efficiency/PCR do to sequence composition). For sex chromosomes, one should apply this function separately to men and women and then recenter the resulting matrix according to the expected copy number.

Usage

sweepMode(x, MARGIN)

## S4 method for signature 'SnpArrayExperiment'
sweepMode(x, MARGIN)

Arguments

x	see showMethods(sweepMode)
MARGIN	integer indicating which margin (1=rows, 2=columns) to sweep the mode

Value

an object of the same class as x

Examples

data(snp_exp)
snp_exp_rowcentered <- sweepMode(snp_exp, 1)
snp_exp_colcentered <- sweepMode(snp_exp, 2)
x <- lrr(snp_exp)
x_rowcentered <- sweep(x, 1, rowModes(x))
all.equal(lrr(snp_exp_rowcentered), x_rowcentered)

VanillaICE documentation built on Nov. 8, 2020, 7:33 p.m.