geneUsage: Gene usage of clones

Description

This function gives information about the gene usage of clones. Results can returned as relative or absolute values and be visualized as a barplot, using plotGeneUsage.

Usage

geneUsage(geneUsage = 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

geneUsage

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 o

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

Details

Vector of genes will be analyzed for one of the levels subgroup (f.e. IGHV1), gene (f.e. IGHV1-1) or allele (f.e. IGHV1-1*2).

The PDF character string should be only the project name (without ".pdf"). For only gene usage, a plot called "PDF"_Gene-usage.pdf will be saved to your working direktory.

If geneUsage.Func = T a figure called "PDF"_Gene-usage_vs_Functionality.pdf will be saved and if geneUsage.JunctionFr = T a figure called "PDF"_Gene-usage_vs_Junction-frame.pdf will be saved.

Examples

Run this code

data(clones.ind)
geneUsage(geneUsage = clones.ind$V_gene, level = "subgroup", 
     functionality = clones.ind$Functionality_all_sequences)
plotGeneUsage(geneUsage = clones.ind$V_gene, 
     functionality = TRUE)