CPSplot: Codon pair score line plot

In alex-sbu/CPBias: Codon pair bias calculation and gene design.

Description

Local codon pair scores plotted as a smooth line along the length of a nucleotide sequence.

Usage

CPSplot(seqOne, refOne, seqTwo = NULL, refTwo = NULL, start = 1,
  end = NULL, windowSize = NULL)

Arguments

seqOne	Sequences can be input directly as a character string or as the file path to a fasta file. All sequences must be in the correct reading frame, stop codons or codons not defined in the translation table are not allowed and will generate an error.
refOne	CPB reference table. See CPBtable.
seqTwo	An alternate codon pair recoding of seqOne. seqTwo only accepts sequences with identical length to seqOne.
refTwo	A second CPB reference. The sequence(s) will be plotted relative to both references.
start	Nucleotide position in the sequence.
end	Nucleotide position in the sequence.
windowSize	Designates the number of nucleotides over which smoothing occurs. If NULL windowSize is 7.5% of the sequence length.

Details

The individual codon pair scores across a gene sequence are plotted as a smooth curve by locally weighted quadratic regression (loess). Span is defined as the window size divided by total sequence length in nucleotides. Two different CPS encodings of a sequence can be compared with up to two reference CPB's.

Value

Line plot in the graphics device.

Examples

fastaLocation <- system.file('tbevns5.fasta', package = 'CPBias')
tbev <- importFasta(fastaLocation)[[1]]

humCPS <- CPScalc(tbev, Homo.sapiens, silent=TRUE, draw=FALSE)[[1]]
tbevhmax <- CPSdesign.dual(tbev, Aedes.aegypti, Homo.sapiens, humCPS, 'max',
draw=FALSE, silent=TRUE)
CPSplot(tbev, Homo.sapiens, tbevhmax[[9]], Homo.sapiens)

alex-sbu/CPBias documentation built on May 11, 2019, 11:24 p.m.