hlaAllele: A list of HLA/KIR types

In HIBAG: HLA Genotype Imputation with Attribute Bagging

Description

Return an object of hlaAlleleClass, which contains HLA/KIR types.

Usage

hlaAllele(sample.id, H1, H2, max.resolution="", locus="any", assembly="auto",
    locus.pos.start=NA_integer_, locus.pos.end=NA_integer_, prob=NULL,
    na.rm=TRUE)

Arguments

sample.id	sample IDs
H1	a vector of HLA/KIR alleles
H2	a vector of HLA/KIR alleles
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 "" indicating no limit on resolution
locus	the name of HLA locus: "A", "B", "C", "DRB1", "DRB5", "DQA1", "DQB1", "DPB1", KIR locus, or "any", where "any" indicates any other multiallelic locus; see hlaLociInfo for possible locus names
assembly	the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning
locus.pos.start	the starting position in basepair
locus.pos.end	the end position in basepair
prob	the probabilities assigned to the samples
na.rm	if TRUE, remove the samples without valid HLA types

Details

The format of H1 and H2 is "allele group : different protein : synonymous mutations in exons : synonymous mutations in introns"L, where the suffix L is express level (N, null; L, low; S, secreted; A, aberrant; Q: questionable). For example, "44:02:01:02L". If max.resolution is specified, the HLA alleles will be trimmed with a possible maximum resolution.

Value

Return a hlaAlleleClass object, and it is a list:

locus	HLA locus
pos.start	the starting position in basepair
pos.end	the end position in basepair
value	a data frame
assembly	the human genome reference, such like "hg19"

The component value includes:

sample.id	sample ID
allele1	HLA allele
allele2	HLA allele
prob	the posterior probability

Author(s)

Xiuwen Zheng

See Also

hlaAlleleDigit, hlaAlleleSubset, hlaLociInfo

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)


# encode other loci
hlaAllele("HD0010", "1", "2", locus="NewLocus")

Example output

HIBAG (HLA Genotype Imputation with Attribute Bagging)
Kernel Version: v1.3
Supported by Streaming SIMD Extensions (SSE2) [64-bit]
  sample.id   A.1   A.2   B.1   B.2   C.1   C.2 DQA1.1 DQA1.2 DQB1.1 DQB1.2
1   NA11882 01:01 29:02 15:01 44:03 06:02 16:01  01:02  03:01  03:02  06:02
2   NA11881 03:01 26:01 07:02 07:02 07:02 07:02  01:02  01:02  06:02  06:02
3   NA11993 26:01 29:02 44:03  <NA> 16:01 16:01  01:01  01:02  05:01  06:02
4   NA11992 01:01 02:01 08:01 35:01 04:01 07:01  01:01  05:01  02:01  05:01
5   NA11995 01:01 01:01 08:01 57:01 06:02 07:01  01:02  01:03  06:02  06:03
6   NA11994 01:01 11:01 07:02 51:01 07:02 15:02  03:01  03:01  03:02  03:02
  DRB1.1 DRB1.2
1  04:01  15:01
2  15:01  15:01
3  01:01  15:01
4  01:01  03:01
5  13:01  15:01
6  04:02  04:04
[1] 60 13
Gene: A
Range: [29910247bp, 29913661bp] on hg19
# of samples: 60
# of unique HLA alleles: 14
# of unique HLA genotypes: 29
using the default genome assembly (assembly="hg19")
$locus
[1] "NewLocus"

$pos.start
[1] NA

$pos.end
[1] NA

$value
  sample.id allele1 allele2
1    HD0010       1       2

$assembly
[1] "hg19"

attr(,"class")
[1] "hlaAlleleClass"

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