geneUsage: Gene usage statistics

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

This function gives information about the gene usage distribution (see detail!). Results can returned as relative or absolute values and be visualized as a barplot, using plotGeneUsage. Further gene usage can be analyzed in relation to functionality or junction frame usage.

Usage

geneUsage(genes = NULL, level = c("subgroup", "gene", "allele"), 
     functionality = NULL, junctionFr = NULL, 
     abundance=c("relative","absolute"), ...)

plotGeneUsage(geneUsage.tab=NULL,plotFunctionality=FALSE,plotJunctionFr=FALSE,
     color=c("orange","darkblue","gray"), title=NULL, PDF=NULL,...)

Arguments

genes	Vector containing gene information (IMGT nomenclature; see Details)
level	Gene level used for gene usage analysis: subgroup, gene, allele
functionality	Vector containing functionality information
junctionFr	Vector containing functionality information
abundance	Shall relative or absolute values be returned? (default: relative)
geneUsage.tab	Output of geneUsage()
plotFunctionality	Shall gene usage vs. functionality be plotted? (default: FALSE)
plotJunctionFr	Shall gene usage vs. junction frame be plotted? (default: FALSE)
color	color used for plots (default: c("orange","darkblue","gray"))
title	title of the plot (optional)
PDF	PDF project name (see Details)
...

Details

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"). For an analysis of the gene usage distribution, a plot called "PDF"_Gene-usage.pdf will be saved to the working direktory.

If geneUsage.Func = T gene usage vs. functionality will be analyzed (and a figure called "PDF"_Gene-usage_vs_Functionality.pdf will be saved) and if geneUsage.JunctionFr = T gene usage vs. junction frame usage will be analyzed (and figure called "PDF"_Gene-usage_vs_Junction-frame.pdf will be saved).

Value

Output is a list containing

gene_usage	relative or absolute abundances of subgroups/genes
gene_usage_vs_functionality	(optional)
gene_usage_vs_junction_frame	(optional)

Note

For large datasets computational time can be extensive.

Author(s)

Julia Bischof

See Also

geneUsage, plotGeneUsage

Examples

data(clones.ind)
geneUsage(genes = clones.ind$V_gene, level = "subgroup", 
     functionality = clones.ind$Functionality_all_sequences)
## Not run: plotGeneUsage(geneUsage.tab = clones.ind$V_gene, 
     plotFunctionality = TRUE)
## End(Not run)

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