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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(crlmm)
Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: preprocessCore
Welcome to crlmm version 1.30.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/crlmm/calculateRBaf.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculateRBaf
> ### Title: Calculate log R ratios and B allele frequencies.
> ### Aliases: calculateRBaf calculateRBaf,CNSet-method
> ### Keywords: list methods
> 
> ### ** Examples
> 
> 	data(cnSetExample)
> 	baf.lrr <- suppressWarnings(calculateRBaf(cnSetExample, "SHELF"))
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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