Description Usage Arguments Value See Also Examples
Group sequences in an MS object by their GC content.
1 | groupByGC.ms(ms, ngroups)
|
ms |
MS object, containing at least ngroups sequences. |
ngroups |
Number of quantiles to group sequences into. |
List of MS objects, where element i represents the i'th quantile according to GC content.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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")
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