hlaSampleAllele: Get sample IDs from HLA types with a filter

In HIBAG: HLA Genotype Imputation with Attribute Bagging

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"))

Example output

HIBAG (HLA Genotype Imputation with Attribute Bagging)
Kernel Version: v1.3
Supported by Streaming SIMD Extensions (SSE2) [64-bit]
Gene: A
Range: [29910247bp, 29913661bp] on hg19
# of samples: 60
# of unique HLA alleles: 14
# of unique HLA genotypes: 29
 [1] "NA11882" "NA11881" "NA11993" "NA11992" "NA11995" "NA11994" "NA12249"
 [8] "NA12248" "NA07055" "NA07034" "NA06985" "NA06993" "NA12057" "NA12056"
[15] "NA12044" "NA12043" "NA11840" "NA11839" "NA12154" "NA12156" "NA12155"
[22] "NA12004" "NA12003" "NA12006" "NA12005" "NA12145" "NA12144" "NA12239"
[29] "NA12146" "NA07000" "NA06994" "NA07056" "NA07022" "NA12234" "NA12264"
[36] "NA07345" "NA07357" "NA11830" "NA11829" "NA11832" "NA11831" "NA12236"
[43] "NA12717" "NA12716" "NA12751" "NA12750" "NA12761" "NA12760" "NA12763"
[50] "NA12762" "NA12813" "NA12812" "NA12815" "NA12814" "NA12873" "NA12872"
[57] "NA12875" "NA12874" "NA12892" "NA12891"
 [1] "NA11992" "NA11995" "NA11994" "NA12248" "NA06985" "NA06993" "NA12057"
 [8] "NA12044" "NA11840" "NA12156" "NA12155" "NA12003" "NA12145" "NA12144"
[15] "NA12146" "NA07056" "NA07022" "NA07345" "NA11830" "NA11829" "NA11831"
[22] "NA12236" "NA12717" "NA12716" "NA12751" "NA12763" "NA12762" "NA12812"
[29] "NA12814" "NA12872" "NA12892"

HIBAG documentation built on March 24, 2021, 6 p.m.