print.hlaAttrBagClass: Summarize a "hlaAttrBagClass" or "hlaAttrBagObj" object.

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Summarize a “hlaAttrBagClass” or “hlaAttrBagObj” object.

Description

Summarize an object of hlaAttrBagClass or hlaAttrBagObj.

Usage

## S3 method for class 'hlaAttrBagClass'
print(x, ...)
## S3 method for class 'hlaAttrBagObj'
print(x, ...)
## S3 method for class 'hlaAttrBagClass'
summary(object, show=TRUE, ...)
## S3 method for class 'hlaAttrBagObj'
summary(object, show=TRUE, ...)

Arguments

x	an object of hlaAttrBagClass or hlaAttrBagObj
object	an object of hlaAttrBagClass or hlaAttrBagObj
show	if TRUE, show information
...	further arguments passed to or from other methods

Value

print returns NULL.

summary.hlaAttrBagClass and summary.hlaAttrBagObj return a list:

num.classifier	the total number of classifiers
num.snp	the total number of SNPs
snp.id	SNP IDs
snp.position	SNP position in basepair
snp.hist	the number of classifier for each SNP, and it could be used for SNP importance
info	a data.frame for the average number of SNPs (num.snp), haplotypes (num.haplo), out-of-bag accuracies (accuracy) among all classifiers: mean, standard deviation, min, max

Author(s)

Xiuwen Zheng

See Also

plot.hlaAttrBagClass, plot.hlaAttrBagObj

Examples

# make a "hlaAlleleClass" object
hla.id <- "C"
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)
# please use "nclassifier=100" when you use HIBAG for real data
model <- hlaAttrBagging(hla, train.geno, nclassifier=2, verbose.detail=TRUE)
print(model)

zhengxwen/HIBAG documentation built on Nov. 24, 2024, 5:24 a.m.