BDstrat {HLAtools}

Stratify BIGDAWG Datasets by Specific Alleles

Description

Divides a BIGDAWG-formatted dataset into two subsets (strata) that do and do not include specified alleles.

Usage

BDstrat(dataset, alleles, warnBelow = 21)

Arguments

dataset

A BIGDAWG-formatted data frame or a path to a BIGDAWG-formatted, tab-delimited text file.

alleles

A vector of allele names in the locus-asterisk-allele_name format (e.g., "A*01:01:01:01").

warnBelow

An integer that defines a low number of subjects in a stratum, generating a warning message. The default value is 21.

Value

A list-object of two BIGDAWG-formatted data frames titled dataset$⁠<alleles>-positive⁠ and dataset$⁠<alleles>-negative⁠. The positive list element includes all subjects with the specified alleles, and the negative list element includes all subjects without those specified alleles.

References

BIGDAWG Data Format

Examples

HLA_data.multi.strat <- BDstrat(sHLAdata,c("DRB1*16:02:01:01","DRB1*04:07:01:01","A*25:01:01:01"))
HLA_data.single.strat <- BDstrat(sHLAdata,"DRB1*16:02:01:01")