hlaAlleleDigit {HIBAG} | R Documentation

## Trim HLA alleles

### Description

Trim HLA alleles to specified width.

### Usage

    hlaAlleleDigit(obj, max.resolution="4-digit", 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": "allele" = "2-digit"; "protein" = "4-digit"; "full" and "" indicating no limit on resolution
`rm.suffix` | whether remove the suffix, e.g., for "01:22N", "N" is a suffix

### Details

Either `HLAtypes` or `H1` `H2` should be specified. The format of `HLAtypes` is "allele 1 / allele 2", e.g., "0512/0102". If `max.resolution` is specified, the HLA alleles will be trimmed with the maximum resolution.

### 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)

[Package HIBAG version 1.16.0 Index]