hlaDistance: Distance matrix of HLA alleles

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Distance matrix of HLA alleles

Description

To calculate the distance matrix of HLA alleles from a HIBAG model.

Usage

hlaDistance(model)

Arguments

model

a model of hlaAttrBagClass or hlaAttrBagObj

Value

Return a distance matrix with row and column names for HLA alleles.

Author(s)

Xiuwen Zheng

Examples

# 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")

# flanking genotypes
train.geno <- hlaGenoSubsetFlank(HapMap_CEU_Geno, hla.id, 500000)
summary(train.geno)

# train a HIBAG model
set.seed(100)
model <- hlaAttrBagging(hla, train.geno, nclassifier=10)
summary(model)

# distance matrix
d <- hlaDistance(model)

# draw
p <- hclust(as.dist(d))
plot(p, xlab="HLA alleles")

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