hlaDistance {HIBAG} | R Documentation |
To calculate the distance matrix of HLA alleles from a HIBAG model.
hlaDistance(model)
model |
a model of |
Return a distance matrix with row and column names for HLA alleles.
Xiuwen Zheng
# 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")