compare.geneUsage: Compare gene usage of different samples

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)

Value

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

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.

Examples

Run this code

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)

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