R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Filtering ChIP-seq reads

chipseqFilter

R Documentation

Filtering ChIP-seq reads

Description

Convenience for creating an SRFilter object appropriate for ChIP-seq data. Typically, the result is passed to readAligned when loading reads.

Usage

chipseqFilter(exclude = "[_MXY]", uniqueness = c("location", "sequence", "location*sequence", "none"), hasStrand = TRUE)

Arguments

`exclude`	A regular expression for excluding chromosomes by name. Just like the parameter to `bsapply`.
`uniqueness`	The criteria used to determine whether a read is unique. A read may be unique if it maps to a unique `location`, has a unique `sequence` or both. Specifying `none` avoids this test entirely.
`hasStrand`	Whether to require that the read is mapped to a strand, which usually translates to whether the read was mapped at all.

Value

An SRFilter object

Author(s)

M. Lawrence

Examples

sp <- SolexaPath(system.file("extdata", package="ShortRead"))

filter <- chipseqFilter()
aln <- readAligned(sp, "s_2_export.txt", filter=filter)
## allow mapping to the same location (but only if sequence is different)
filter <- chipseqFilter(uniqueness = "sequence")
aln <- readAligned(sp, "s_2_export.txt", filter=filter)
## allow sex chromosomes
filter <- chipseqFilter(exclude = "[M_]")
aln <- readAligned(sp, "s_2_export.txt", filter=filter)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/chipseqFilter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chipseqFilter
> ### Title: Filtering ChIP-seq reads
> ### Aliases: chipseqFilter
> 
> ### ** Examples
> 
> sp <- SolexaPath(system.file("extdata", package="ShortRead"))
> 
> filter <- chipseqFilter()
> aln <- readAligned(sp, "s_2_export.txt", filter=filter)
> ## allow mapping to the same location (but only if sequence is different)
> filter <- chipseqFilter(uniqueness = "sequence")
> aln <- readAligned(sp, "s_2_export.txt", filter=filter)
> ## allow sex chromosomes
> filter <- chipseqFilter(exclude = "[M_]")
> aln <- readAligned(sp, "s_2_export.txt", filter=filter)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>