Get the GC content of target ranges from a reference FASTA file

Description

A short function using scanFa from the Rsamtools package on a target GRanges and a reference FASTA file

Usage

  getGCcontent(target, reference.file)

Arguments

Value

Returns a vector of the ratio of G and C basepairs to total basepairs (not counting N's).

Examples

  target.file <- system.file("extdata","targets.bed",package="exomeCopy")
  target.df <- read.delim(target.file,header=FALSE,col.names=c("seqname","start","end")) 
  target <- GRanges(seqname=target.df$seqname,IRanges(start=target.df$start+1,end=target.df$end))
  reference.file <- system.file("extdata","reference.fa",package="exomeCopy")
  GCcontent <- getGCcontent(target, reference.file)

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(exomeCopy)
Loading required package: IRanges
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/exomeCopy/getGCcontent.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getGCcontent
> ### Title: Get the GC content of target ranges from a reference FASTA file
> ### Aliases: getGCcontent
> 
> ### ** Examples
> 
>   target.file <- system.file("extdata","targets.bed",package="exomeCopy")
>   target.df <- read.delim(target.file,header=FALSE,col.names=c("seqname","start","end")) 
>   target <- GRanges(seqname=target.df$seqname,IRanges(start=target.df$start+1,end=target.df$end))
>   reference.file <- system.file("extdata","reference.fa",package="exomeCopy")
>   GCcontent <- getGCcontent(target, reference.file)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>