Find peaks with extreme count values

Description

findOutliers uses the function boxplot to determine outlier peaks with extreme high total counts in each sample.

Usage

findOutliers(DBA, range = 20, draw.on=TRUE)

Arguments

Value

DBA object, with additional list element Filter added to MD.

Author(s)

Gabriele Schweikert

See Also

getPeakProfiles, boxplot

Examples

data(Cfp1Profiles)
Cfp1 <- findOutliers(Cfp1Profiles, range=20)
Filter <- Cfp1$MD$Filter


Cfp1Strict <- findOutliers(Cfp1Profiles, range=10)
OutlierPeakIDs <- Cfp1Strict$MD$Filter$HighPeakIds

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MMDiff)
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: DiffBind
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: GMD
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Warning message:
Package 'MMDiff' is deprecated and will be removed from Bioconductor
  version 3.4 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MMDiff/findOutliers.Rd_%03d_medium.png", width=480, height=480)
> ### Name: findOutliers
> ### Title: Find peaks with extreme count values
> ### Aliases: findOutliers
> 
> ### ** Examples
> 
> data(Cfp1Profiles)
> Cfp1 <- findOutliers(Cfp1Profiles, range=20)
Error in dev.new() : no suitable unused file name for pdf()
Calls: findOutliers -> dev.new
Execution halted