compute_gc: Compute the GC content of DNA and probe sequences

In Ringo: R Investigation of ChIP-chip Oligoarrays

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

probe.sequences	character vector of DNA or probe sequences of which the GC content is to be computed
digits	integer specifying the desired precision

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)

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.