Compute the GC content of DNA and probe sequences

Description

Simple auxiliary function to compute the GC content of a given set of DNA sequences, such as microarray probe sequences.

Usage

compute.gc(probe.sequences, digits = 2)

Arguments

Value

a numeric vector with sequence-wise GC contents; the names of this vector are the names of the supplied probe.sequences.

Author(s)

Joern Toedling

See Also

Function basecontent in package matchprobes for a more general function to compute base occurrence in sequences

Examples

  ex.seqs <- c("gattaca", "GGGNTT", "ggAtT", "tata","gcccg")
  names(ex.seqs) <- paste("sequence",1:5,sep="")
  compute.gc(ex.seqs)

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(Ringo)
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Ringo/compute_gc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: compute.gc
> ### Title: Compute the GC content of DNA and probe sequences
> ### Aliases: compute.gc gccontent
> ### Keywords: manip
> 
> ### ** Examples
> 
>   ex.seqs <- c("gattaca", "GGGNTT", "ggAtT", "tata","gcccg")
>   names(ex.seqs) <- paste("sequence",1:5,sep="")
>   compute.gc(ex.seqs)
sequence1 sequence2 sequence3 sequence4 sequence5 
     0.29      0.50      0.40      0.00      1.00 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>