Generate median background read depth

Description

Normalizes a set of columns representing read counts from different samples by their mean. Then calculates a statistic across the rows of normalized counts.

Usage

  generateBackground(sample.names, rdata, fn=median)

Arguments

Value

The value of fn applied across the rows of normalized read counts.

Examples

  data(exomecounts)
  sample.names <- grep("HG.+",colnames(exomecounts),value=TRUE)
  exomecounts[["bg"]] <- generateBackground(sample.names, exomecounts,
median) 
  exomecounts[["bg.sd"]] <- generateBackground(sample.names,
exomecounts, sd) 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(exomeCopy)
Loading required package: IRanges
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: 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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/exomeCopy/generateBackground.Rd_%03d_medium.png", width=480, height=480)
> ### Name: generateBackground
> ### Title: Generate median background read depth
> ### Aliases: generateBackground
> 
> ### ** Examples
> 
>   data(exomecounts)
>   sample.names <- grep("HG.+",colnames(exomecounts),value=TRUE)
>   exomecounts[["bg"]] <- generateBackground(sample.names, exomecounts,
+ median) 
>   exomecounts[["bg.sd"]] <- generateBackground(sample.names,
+ exomecounts, sd) 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>