compare.aaDistribution: Compare amino acid distribution of different samples

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

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)

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.

Value

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

Note

For large datasets computational time can be extensive.

Author(s)

Julia Bischof

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)

bcRep documentation built on May 2, 2019, 5:14 a.m.