gene_comb_funk: gene/gene ratios of two gene families

In BCellMA: B Cell Receptor Somatic Hyper Mutation Analysis

Description

The calculation was obtained according bcRep package in R language. Every combination of two families was summarized and divided by the sum of all combinations across each group.

Usage

gene_comb_funk(family1, family2)

Arguments

family1	"V_GENE_and_allele" colums from IMGT/HighV-Quest table 1 coled "1_Summary.txt"
family2	"J_GENE_and_allele" or "D_GENE_and_allele" colums from IMGT/HighV-Quest table 1 coled "1_Summary.txt"

Value

Output is the data matrix of gene/gene ratios of two gene families.

References

Bischof J. and Ibrahim SM. bcRep: R Package for Comprehensive Analysis of B Cell Receptor Repertoire Data. PLoS One. 11(8):e0161569, 2016. doi: 10.1371/journal.pone.0161569.

Examples

data(IMGTtab1)
gane_comb<-gene_comb_funk(family1 = IMGTtab1$V_GENE_and_allele,
                          family2 = IMGTtab1$J_GENE_and_allele)
gane_comb

BCellMA documentation built on May 1, 2019, 7:58 p.m.