oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
g2.coord = system.file("sequences/ct.coord", package = "seqinr"),
oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)
g2num
for the CDS number in
the g2.coord
file, start.kb
for the start position of CDS
expressed in Kb (this is the position of the first occurence of a
nucleotide in a CDS regardless of its orientation), end.kb
for the last position of a CDS, CDS.excess
for the DNA walk for
gene orientation (+1 for a CDS in the direct strand, -1 for a CDS in
the reverse strand) cummulated over genes, skew
for the cummulated
composite skew in third codon positions, x
for the cummulated
T - A skew in third codon position, y
for the cummulated C - G
skew in third codon positions.To have an overview of the seqinR's functionnality, please consult this vignette: Charif, D., Lobry, J.R. (2005) SeqinR: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Springer Verlag, Biological and Medical Physics/Biomedical Series, in preparation.
out <- oriloc()
plot(out$st, out$sk, type="l", xlab="Map position in Kb",
ylab = "Cumulated composite skew",
main=expression(italic(Chlamydia~~trachomatis)~~complete~~genome))
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