sequences.geneComb: Gene/gene combinations
In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function calculates the abundance of two paired gene families. Analysis can be done for subgroup, gene and allele level (see Details).

sequences.geneComb returns a data frame containing all possible combinations of gene families 1 (rows) and 2 (columns) in relative or absolute values.

plotGeneComb visualizes relative abundances of gene/gene combinations in a heatmap. Absolute values will be converted to relative abundances.

sequences.geneComb(family1 = NULL, family2 = NULL, 
     level = c("subgroup","gene","allele"), abundance = c("relative", "absolute"),
     nrCores=1)
     
plotGeneComb(geneComb.tab=NULL,color=c("gray97","darkblue"),withNA=TRUE, 
     title=NULL, PDF=NULL,...)

`family1`	Vector including gene family 1, should be matched to order of family2 (see Details)
`family2`	Vector including gene family 2, should be matched to order of family1 (see Details)
`level`	Gene family level: subgroup, gene or allele (see Details)
`abundance`	How values shall be returned: relative or absolute abundance.
`nrCores`	Number of cores used for parallel processing (default: 1)
`geneComb.tab`	Output data frame from `sequences.genecomb()`
`color`	colors of heatmap (default: gray and blue)
`withNA`	Shall combination without information for one of both families be included? (default: TRUE)
`title`	title of plot (NULL: "family1 & family2 gene combinations (zoom: xx)"; turn of with "")
`PDF`	PDF project name (see Details)
`...`

Input are vectors of IMGT/HighV-QUEST output file 1_Summary(...).txt. Columns like "V-GENE and allele", "D-GENE and allele" or "J-GENE and allele" can be used as input, but need to have the same order! Levels can be subgroup (e.g. IGHV1), genes (e.g. IGHV1-1) or alleles (e.g. IGHV1-1*2).

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

A figure called "PDF"_"family1"-"family2"-combinations.pdf will be saved to the working directory.

Output is a data frame containing gene/gene combinations, with family 1 as rows and family 2 as columns. Either in absolute or relative abundances.

For large datasets computational time can be extensive.

Julia Bischof

IMGT Repertoire (IG and TR): http://www.imgt.org/IMGTrepertoire/LocusGenes/

sequences.geneComb, plotGeneComb, geneUsage

data(summarytab)
VDcomb.tab<-sequences.geneComb(family1 = summarytab$V_GENE_and_allele, 
     family2 = summarytab$D_GENE_and_allele, level = "subgroup", abundance = "relative")
     
plotGeneComb(geneComb.tab=VDcomb.tab, withNA=FALSE)