geneUsage: Gene usage statistics

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)

...

Value

Output is a list containing

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).

Examples

Run this code

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)