hlaSampleAllele: Get sample IDs from HLA types with a filter

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Get sample IDs from HLA types with a filter

Description

Get sample IDs from HLA types limited to a set of HLA alleles.

Usage

hlaSampleAllele(TrueHLA, allele.limit=NULL, max.resolution="")

Arguments

TrueHLA	an object of hlaAlleleClass
allele.limit	a list of HLA alleles, the validation samples are limited to those having HLA alleles in allele.limit, or NULL for no limit. allele.limit could be character-type, hlaAttrBagClass or hlaAttrBagObj
max.resolution	"2-digit", "4-digit", "6-digit", "8-digit", "allele", "protein", "2", "4", "6", "8", "full" or "": "allele" = "2-digit", "protein" = "4-digit", "full" and "" mean no limit on resolution

Value

Return a list of sample IDs.

Author(s)

Xiuwen Zheng

See Also

hlaCompareAllele

Examples

# make a "hlaAlleleClass" object
hla.id <- "A"
hla <- hlaAllele(HLA_Type_Table$sample.id,
    HLA_Type_Table[, paste(hla.id, ".1", sep="")],
    HLA_Type_Table[, paste(hla.id, ".2", sep="")],
    locus=hla.id, assembly="hg19")
summary(hla)

hlaSampleAllele(hla)

hlaSampleAllele(hla, allele.limit=c(
    "01:01","02:01","02:06", "03:01", "11:01", "23:01"))

zhengxwen/HIBAG documentation built on Nov. 24, 2024, 5:24 a.m.