hlaCheckSNPs {HIBAG} | R Documentation

## Check the SNP predictors in a HIBAG model

### Description

Check the SNP predictors in a HIBAG model, by calculating the overlapping between the model and SNP genotypes.

### Usage

    hlaCheckSNPs(model, object,
        match.type=c("RefSNP+Position", "RefSNP", "Position"), verbose=TRUE)

### Arguments

`model` | an object of `hlaAttrBagClass`, or an object of `hlaAttrBagObj`
`object` | a genotype object of `hlaSNPGenoClass`, or a character vector like c("rs2523442", "rs9257863", ...)
`match.type` | `"RefSNP+Position"` (by default) – using both of RefSNP IDs and positions; `"RefSNP"` – using RefSNP IDs only; `"Position"` – using positions only
`verbose` | if TRUE, show information

### Value

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

### Author(s)

Xiuwen Zheng

### See Also

`hlaAttrBagging`, `predict.hlaAttrBagClass`

### Examples

    # 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)

[Package HIBAG version 1.22.0 Index]