A function to identify and produce summary statistics for differentially expressed peaks.

Description

Given two sets of peaks, this function combines them and summarizes the individual coverage vectors under the combined peak set.

Usage

diffPeakSummary(ranges1, ranges2,
                viewSummary = list(sums = viewSums, maxs = viewMaxs))

Arguments

Value

A data.frame with one row for each peak in the combined data. The chromosome, start and stop nucleotide positions (+ strand) are given as are the summary statistics requested.

Author(s)

D. Sarkar

Examples

data(cstest)
library(BSgenome.Mmusculus.UCSC.mm9)
seqlevels(cstest) <- seqlevels(Mmusculus)
seqlengths(cstest) <- seqlengths(Mmusculus)
## find peaks
findPeaks <- function(reads) {
  reads.ext <- resize(reads, width = 200)
  slice(coverage(reads.ext), lower = 8)
}
peakSummary <- diffPeakSummary(findPeaks(cstest$gfp), findPeaks(cstest$ctcf))

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
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> library(chipseq)
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: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomicAlignments
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chipseq/diffPeakSummary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: diffPeakSummary
> ### Title: A function to identify and produce summary statistics for
> ###   differentially expressed peaks.
> ### Aliases: diffPeakSummary
> ###   diffPeakSummary,RleViewsList,RleViewsList-method
> 
> ### ** Examples
> 
> data(cstest)
> library(BSgenome.Mmusculus.UCSC.mm9)
Loading required package: BSgenome
Loading required package: rtracklayer
> seqlevels(cstest) <- seqlevels(Mmusculus)
> seqlengths(cstest) <- seqlengths(Mmusculus)
> ## find peaks
> findPeaks <- function(reads) {
+   reads.ext <- resize(reads, width = 200)
+   slice(coverage(reads.ext), lower = 8)
+ }
> peakSummary <- diffPeakSummary(findPeaks(cstest$gfp), findPeaks(cstest$ctcf))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>