groupByGC.ms: Group sequences by GC

Description Usage Arguments Value See Also Examples

View source: R/tfbs.R

Description

Group sequences in an MS object by their GC content.

Usage

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groupByGC.ms(ms, ngroups)

Arguments

ms

MS object, containing at least ngroups sequences.

ngroups

Number of quantiles to group sequences into.

Value

List of MS objects, where element i represents the i'th quantile according to GC content.

See Also

read.ms

Examples

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require("rtfbs")
exampleArchive <- system.file("extdata", "NRSF.zip", package="rtfbs")
seqFile <- "input.fas"
unzip(exampleArchive, seqFile)
# Read in FASTA file "input.fas" from the examples into an 
#   MS (multiple sequences) object
seqs <- read.ms(seqFile)
# Group sequences from the "seqs" MS object based on each 
#   sequences's GC content into 4 new MS objects, one for
#   each GC content range
groups <- groupByGC.ms(seqs, 4)
sapply(groups, length)
sapply(groups, function(x) {range(gcContent.ms(x))})
unlink("input.fas")

rtfbs documentation built on Jan. 22, 2020, 1:07 a.m.