hlaAlleleDigit: Trim HLA alleles

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Trim HLA alleles

Description

Trim HLA alleles to specified width.

Usage

hlaAlleleDigit(obj, max.resolution=NA_character_, rm.suffix=FALSE)

Arguments

obj	should be a hlaAlleleClass object or characters
max.resolution	"2-digit", "1-field", "4-digit", "2-field", "6-digit", "3-field", "8-digit", "4-field", "allele", "protein", "full", "none", or "": "allele" = "2-digit"; "protein" = "4-digit"; "full", "none" or "" for no limit on resolution
rm.suffix	whether remove the non-digit suffix in the last field, e.g., for "01:22N", "N" is a non-digit suffix

Details

If max.resolution is specified, the HLA alleles will be trimmed with the maximum resolution. See https://hla.alleles.org/nomenclature/naming.html for the HLA nomenclature.

Value

Return a hlaAlleleClass object if obj is hlaAlleleClass-type, or characters if obj is character-type.

Author(s)

Xiuwen Zheng

See Also

hlaAllele

Examples

head(HLA_Type_Table)
dim(HLA_Type_Table)  # 60 13

# make a "hlaAlleleClass" object
hla.id <- "A"
hla <- hlaAllele(HLA_Type_Table$sample.id,
    H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")],
    H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")],
    locus = hla.id, assembly="hg19")
summary(hla)

hla2 <- hlaAlleleDigit(hla, "2-digit")
summary(hla2)

zhengxwen/HIBAG documentation built on April 16, 2024, 8:41 a.m.