Sweep the modal log R ratio (by row or column) from a matrix of log R ratios

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

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(VanillaICE)
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

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

Welcome to VanillaICE version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/VanillaICE/sweepMode.Rd_%03d_medium.png", width=480, height=480)
> ### Name: sweepMode
> ### Title: Sweep the modal log R ratio (by row or column) from a matrix of
> ###   log R ratios
> ### Aliases: sweepMode sweepMode,SnpArrayExperiment-method
> 
> ### ** 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)
[1] TRUE
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>