bcRep (version 1.3.6)

compare.aaDistribution: Compare amino acid distribution of different samples

Description

This function compares the amino acid distribution of different samples. Sequences of the same length are clustered and analyzed. Additionally the number of sequences for each sample can be returned. Parallel processing is possible.

Usage

compare.aaDistribution(sequence.list = NULL, names = NULL, numberSeq = FALSE,  nrCores = 1)
plotCompareAADistribution(comp.tab = NULL, plotSeqN = FALSE, colors = NULL,  title = NULL, PDF = NULL)

Arguments

sequence.list

A list containing vectors of amino acid sequences of each sample

names

A vector containing names for the samples (default: Sample1, Sample2, ...)

numberSeq

Shall number of sequences used for analysis be returned? (default: FALSE)

nrCores

Number of cores used for parallel processing

comp.tab

Output tab from compare.aaDistribution()

plotSeqN

Shall number of sequences used for analysis be plotted? (only possible, if in compare.aaDistribution(...,numberSeq=TRUE,...) is used; default: FALSE)

colors

colors used for individuals in sequence number plot (default: rainbow)

title

Title of plot

PDF

PDF project name (see Details)

Value

Output is a list containing amino acid distributions for each sequence length and each sample.

Details

Amino acid distribution for each individual is analyzed. Sequenzes of the same length are clustered and amino acid distribution for each position is measured.

The PDF character string should be only the project name (without ".pdf").

A figure called "PDF"_Comparison_Amino-acid-distribution.pdf will be saved to the working directory.

Optional another figure called PDF"_Comparison_Number-of-sequences.pdf" will be returned.

See Also

compare.aaDistribution, plotCompareAADistribution, aaDistribution

Examples

data(aaseqtab)
data(aaseqtab2)

AAdistr.comp<-compare.aaDistribution(sequence.list = list(aaseqtab$CDR3_IMGT, 
     aaseqtab2$CDR3_IMGT), names = c("IndA", "IndB"), numberSeq = FALSE, nrCores = 1)
## Not run: 
# plotCompareAADistribution(comp.tab = AAdistr.comp, plotSeqN = FALSE, PDF = "Example")
# ## End(Not run)