bcRep (version 1.3.6)

sequences.geneComb: Gene/gene combinations

Description

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.

Usage

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,...)

Arguments

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)

...

Value

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.

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.

References

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

See Also

sequences.geneComb, plotGeneComb, geneUsage

Examples

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)