hlaCheckSNPs {HIBAG} | R Documentation |
Check the SNP predictors in a HIBAG model, by calculating the overlapping between the model and SNP genotypes.
hlaCheckSNPs(model, object, match.type=c("RefSNP+Position", "RefSNP", "Position"), verbose=TRUE)
model |
an object of |
object |
a genotype object of |
match.type |
|
verbose |
if TRUE, show information |
Return a data.frame
for individual classifiers:
NumOfValidSNP |
the number of non-missing SNPs in an individual classifier |
NumOfSNP |
the number of SNP predictors in an individual classifier |
fraction |
NumOfValidSNP / NumOfSNP |
Xiuwen Zheng
hlaAttrBagging
, predict.hlaAttrBagClass
# make a "hlaAlleleClass" object hla.id <- "DQB1" hla <- hlaAllele(HLA_Type_Table$sample.id, H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")], H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")], locus=hla.id, assembly="hg19") # training genotypes region <- 100 # kb snpid <- hlaFlankingSNP(HapMap_CEU_Geno$snp.id, HapMap_CEU_Geno$snp.position, hla.id, region*1000, assembly="hg19") train.geno <- hlaGenoSubset(HapMap_CEU_Geno, snp.sel = match(snpid, HapMap_CEU_Geno$snp.id)) # train a HIBAG model set.seed(1000) model <- hlaAttrBagging(hla, train.geno, nclassifier=2) print(model) hlaCheckSNPs(model, train.geno) # close the HIBAG model explicitly hlaClose(model)