CPScalc: Codon pair score calculator

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

Description

Calculate the codon pair score of a sequence relative to a reference codon pair bias.

Usage

CPScalc(sequence, reference, start = 1, end = NULL, draw = TRUE,
  windowSize = NULL, silent = FALSE)

Arguments

sequence	Sequences can be input directly as a character string or as the file path to a fasta file.
reference	Reference CPB table. See CPBtable.
start	Nucleotide position in the sequence marking the region of the sequence to use for calculation.
end	Nucleotide position in the sequence marking the region of the sequence to use for calculation.
draw	If TRUE, a line plot showing the local CPS along the length of the sequence is output to the graphics device.
windowSize	CPS line plots are smoothed by locally weighted polynomial regression where windowSize designates the number of nucleotides over which individual codon pair scores are smoothed. If NULL, smoothing spans 7.5% of the sequence length.
silent	If TRUE the progress bar is suppressed.

Value

An invisible list is returned:

averageCPS	Average of the individual codon pair scores of the input sequence.
totalCPS	Numeric vector containing the individual codon pair scores along the sequence length.

Examples

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

# Can plot a smoothed line plot with CPScalc output as it is done in
# CPSplot()
CPSx <- 1:length(tbevCPS[[2]])
smoothCPS <- loess(tbevCPS[[2]] ~ CPSx, span = (.05), degree = 2)
lineCPS <- predict(smoothCPS)
plot(lineCPS, type='l')

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