calculateRBaf: Calculate log R ratios and B allele frequencies.

In crlmm: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Description

Calculate log R ratios and B allele frequencies from a CNSet object

Usage

calculateRBaf(object, batch.name, chrom)

Arguments

object	A CNSet object.
batch.name	A character string indicating the batch. If missing, log R ratios and B allele frequencies are calculated for all batches in the object.
chrom	Integer indicating which chromosome to process. If missing, B allele frequencies and log R ratios are calculated for all autosomal chromosomes and chromosome X that are included in object.

Details

batch.name must be a value in batch(object). Currently, one must specify a single batch.name. If a character vector for batch.name is supplied, only the first is evaluated.

TODO: A description of how these values are calculated.

Value

A named list.

baf: Each element in the baf list is a matrix of B allele frequencies (one matrix for each chromosome).

lrr: Each element in the lrr list is a matrix of log R ratios (one matrix for each chromosome).

The log R ratios were scaled by a factor of 100 and stored as an integer. B allele frequencies were scaled by a factor of 1000 and stored as an integer.

Author(s)

Lynn Mireless

References

Peiffer et al., High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping (2006), Genome Research

Examples

	data(cnSetExample)
	baf.lrr <- suppressWarnings(calculateRBaf(cnSetExample, "SHELF"))
	hist(baf.lrr[["baf"]][[1]]/1000, breaks=100)
	hist(baf.lrr[["lrr"]][[1]]/100, breaks=100)
	## Not run: 
		library(ff)
		baf.lrr <- suppressWarnings(calculateRBaf(cnSetExample, "SHELF"))
		class(baf.lrr[["baf"]][[1]]) ## ff_matrix
		class(baf.lrr[["lrr"]][[1]]) ## ff_matrix
	
## End(Not run)

crlmm documentation built on Nov. 8, 2020, 4:55 p.m.