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Last data update: 2014.03.03

R: Combine the counts of both fragment ends.

combineFragEnds

R Documentation

Combine the counts of both fragment ends.

Description

combineFragEnds combines the counts of both fragment ends. A multiplication factor can be used for fragments that only have counts for one valid fragment end.

Usage

combineFragEnds(object, multFactor = 1, filter = FALSE)

Arguments

`object`	A `FourC` object.
`multFactor`	Multiplication factor that can be used to multiply the counts of fragments which only have one valid end. Default is `1`. `filter` is automatically set to `TRUE` if `multFactor` is different from 1.
`filter`	If filter is `TRUE`, only reads from valid fragment ends are summed up for each fragment. This means if only one fragment end is valid only counts from this end are considered. If filter is `FALSE`, counts from both fragment ends are summed up without any filtering.

Value

Returns an updated FourC object with a new assay counts containing the combined count data of both fragment ends for all viewpoints.

Author(s)

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

Examples

data(fc, package="FourCSeq")

fc <- combineFragEnds(fc)
fc

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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/combineFragEnds.Rd_%03d_medium.png", width=480, height=480)
> ### Name: combineFragEnds
> ### Title: Combine the counts of both fragment ends.
> ### Aliases: combineFragEnds
> 
> ### ** Examples
> 
> data(fc, package="FourCSeq")
> 
> fc <- combineFragEnds(fc)
> fc
class: FourC 
dim: 57253 6 
metadata(7): projectPath fragmentDir ... primerFile bamFilePath
assays(3): counts countsLeftFragmentEnd countsRightFragmentEnd
rownames: NULL
rowData names(4): leftSize rightSize leftValid rightValid
colnames(6): ap_WE_68h_1 ap_WE_68h_2 ... ap_WE_34h_1 ap_WE_34h_2
colData names(21): viewpoint condition ... mappedReads mappingRatio
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>