tests/groupByGC_ms.R

In rtfbs: Transcription Factor Binding Site Identification Tool

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")