calculateRBaf {crlmm} | R Documentation

## Calculate log R ratios and B allele frequencies.

### 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)

[Package crlmm version 1.46.0 Index]