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Last data update: 2014.03.03

R: show ChIP-chip data aligned over genome features, e.g. TSSs

quantilesOverPositions

R Documentation

show ChIP-chip data aligned over genome features, e.g. TSSs

Description

Function to show the ChIP-chip data aligned over certain genome features, for example transcription start sites (TSSs).

Usage

quantilesOverPositions(xSet, selGenes, g2p,
                       positions = seq(-5000, 10000, by = 250),
                       quantiles = c(0.1, 0.5, 0.9))

Arguments

`xSet`	an `ExpressionSet` holding the ChIP-chip data
`selGenes`	character; vector of genome features, e.g. transcripts, to use for the plot
`g2p`	A list object containing the mapping between genome positions and probes on the microarray. Created with the function `features2Probes`.
`positions`	Numeric vector of positions related to the coordinates of the genome features, such as in which distances of the TSS the values should be computed over the aligned data
`quantiles`	numeric; which quantiles to compute over the aligned data

Value

An object of class qop, which can be visualized by its plot method.

Author(s)

Joern Toedling

Examples

  ringoExampleDir <- system.file("exData",package="Ringo")
  load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
  trans2Probe <- features2Probes(exGFF, exProbeAnno)
  load(file.path(ringoExampleDir,"exampleX.rda"))
  exampleSX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
     modColumn = "Cy5", allChr = "9", winHalfSize = 400)
  exampleC <- findChersOnSmoothed(exampleSX, probeAnno=exProbeAnno,
     thresholds=0.2, allChr="9", distCutOff=600, cellType="human")
  exampleC <- relateChers(exampleC, exGFF)
  exampleQop <- quantilesOverPositions(exampleSX,
     selGenes=getFeats(exampleC), quantiles=c(0.5, 0.9),
     g2p=trans2Probe, positions=seq(-4000, 1000, by=250))
  show(exampleQop)
  plot(exampleQop, ylim=c(-0.5, 2.1))

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(Ringo)
Loading required package: Biobase
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")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Ringo/quantilesOverPositions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: quantilesOverPositions
> ### Title: show ChIP-chip data aligned over genome features, e.g. TSSs
> ### Aliases: quantilesOverPositions
> ### Keywords: manip
> 
> ### ** Examples
> 
>   ringoExampleDir <- system.file("exData",package="Ringo")
>   load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
>   trans2Probe <- features2Probes(exGFF, exProbeAnno)
Chromosome 9 ... >   load(file.path(ringoExampleDir,"exampleX.rda"))
>   exampleSX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
+      modColumn = "Cy5", allChr = "9", winHalfSize = 400)

Chromosome 9 ...
Suz12_vs_total ... 
Construction result ExpressionSet...Done.
>   exampleC <- findChersOnSmoothed(exampleSX, probeAnno=exProbeAnno,
+      thresholds=0.2, allChr="9", distCutOff=600, cellType="human")


Sample:  Suz12_vs_total.sm ...

Chr: 9 ...>   exampleC <- relateChers(exampleC, exGFF)
Relating 3 ChIP-enriched regions to GFF:
>   exampleQop <- quantilesOverPositions(exampleSX,
+      selGenes=getFeats(exampleC), quantiles=c(0.5, 0.9),
+      g2p=trans2Probe, positions=seq(-4000, 1000, by=250))
>   show(exampleQop)
Quantiles over relative positions for 1 samples:
Suz12_vs_total.sm
Positions:
 -4000 -3750 -3500 -3250 -3000 -2750 -2500 -2250 -2000 -1750 -1500 -1250 -1000 -750 -500 -250 0 250 500 750 1000
Quantiles:
 0.5 0.9
based on 7 genes.
>   plot(exampleQop, ylim=c(-0.5, 2.1))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>