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Last data update: 2014.03.03

R: GC content computation for BSgenome

GCcontent

R Documentation

GC content computation for BSgenome

Description

Compute GC content in a certain region of a BSgenome object

Usage

GCcontent(obj, ..., view.width, as.prob = TRUE)

Arguments

`obj`	BSgenome object
`...`	Arguments passed to getSeq method for BSgenome package.
`view.width`	Passed to `letterFrequencyInSlidingView`, the constant (e.g. 35, 48, 1000) size of the "window" to slide along `obj`. The specified `letters` are tabulated in each window of length `view.width`. The rows of the result (see value) correspond to the various windows.
`as.prob`	If TRUE return percentage of GC content, otherwise return counts.

Details

GC content is an interesting variable may be related to various biological questions. So we need a way to compute GC content in a certain region of a reference genome. GCcontent function is a wrapper around getSeq function in BSgenome package and letterFrequency, letterFrequencyInSlidingView in Biostrings package.

if the view.width is specified, the GC content will be computed in the sliding view

Value

Numeric value indicate count or percentage

Author(s)

Tengfei Yin

Examples

library(BSgenome.Hsapiens.UCSC.hg19)
GCcontent(Hsapiens, GRanges("chr1", IRanges(1e6, 1e6 + 1000)))

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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> library(biovizBase)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biovizBase/GCcontent.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GCcontent
> ### Title: GC content computation for BSgenome
> ### Aliases: GCcontent
> 
> ### ** Examples
> 
> library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> GCcontent(Hsapiens, GRanges("chr1", IRanges(1e6, 1e6 + 1000)))
           C|G
[1,] 0.7162837
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>