hlaCheckSNPs: Check the SNP predictors in a HIBAG model

In HIBAG: HIBAG -- HLA Genotype Imputation with Attribute Bagging

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

HIBAG documentation built on May 2, 2019, 4:50 p.m.