Plot differences

Description

plotDifferences generate plots to investigate the results of getDifferences

Usage

plotDifferences(object, plotWindows = c(1e+05, 1e+06), textsize = 20,
  diffThresh = 0.01, controls = NULL, txdb = NULL, conditionAB = NULL)

Arguments

Author(s)

Felix A. Klein, felix.klein@embl.de

See Also

FourC, getDifferences

Examples

data(fcf, package="FourCSeq")

fcf <- getDifferences(fcf, referenceCondition="WE_68h")

plotDifferences(fcf)

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(FourCSeq)
Loading required package: GenomicRanges
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: GenomeInfoDb
Loading required package: ggplot2
Loading required package: DESeq2
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")'.

Loading required package: splines
Loading required package: LSD
Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/FourCSeq/plotDifferences.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDifferences
> ### Title: Plot differences
> ### Aliases: plotDifferences
> 
> ### ** Examples
> 
> data(fcf, package="FourCSeq")
> 
> fcf <- getDifferences(fcf, referenceCondition="WE_68h")
[1] "ap"
found already estimated dispersions, replacing these
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
> 
> plotDifferences(fcf)
[1] "ap"
Successfully plotted results.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>