compare.geneUsage: Compare gene usage of different samples

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

This function compares the gene usage of different samples (see details!). Analysis can be done for subgroups, genes and alleles (see Details). Values can be returned as relative or absolute abundance. Parallel processing is possible.

Usage

compare.geneUsage(gene.list = NULL, level = c("subgroup", "gene", "allele"), 
     abundance = c("relative", "absolute"), names = NULL, nrCores = 1)

plotCompareGeneUsage(comp.tab = NULL, color = c("gray97", "darkblue"), 
     title = NULL, PDF = NULL)

Arguments

gene.list	A list containing vectors of genes of each sample
level	Gene level used for gene usage analysis: subgroup, gene, allele
abundance	Shall relative or absolute values be returned? (default: relative)
names	A vector containing names for the samples (default: like Sample1, Sample2, ...)
nrCores	Number of cores used for parallel processing
comp.tab	Output tab from compare.geneUsage()
color	Colors used for heatmap (default: gray and darkblue)
title	Title of plot
PDF	PDF project name (see Details)

Details

Gene usage analysis will be done for each sample. Vector of genes will be analyzed for one of the levels subgroup (e.g. IGHV1), gene (e.g. IGHV1-1) or allele (e.g. IGHV1-1*2). Proportions (abundance = "relative") are always based on the number of all alleles found in list: the number of the subgroup/gene/allele is divided by the number of all alleles mentioned for all sequences (in the case there are more alleles/genes mentioned for one sequence).

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

A figure called "PDF"_Comparison_Gene-usage.pdf will be saved to the working directory.

Value

Output is a data frame containing absolue or relative values of gene usage of each sample.

Note

For large datasets computational time can be extensive.

Author(s)

Julia Bischof

See Also

geneUsage, compare.geneUsage, plotCompareGeneUsage

Examples

data(aaseqtab)
data(aaseqtab2)

Vgenes.comp<-compare.geneUsage(gene.list = list(aaseqtab$V_GENE_and_allele, 
     aaseqtab2$V_GENE_and_allele), level = "subgroup", abundance = "relative", 
     names = c("IndA", "IndB"), nrCores = 1)
## Not run: 
plotCompareGeneUsage(comp.tab = Vgenes.comp, color = c("gray97", "darkblue"), PDF = "Example")

## End(Not run)

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