hlaAttrBagObj: The class of HIBAG object

In HIBAG: HLA Genotype Imputation with Attribute Bagging

Description

The class of a HIBAG object, which can be saved in the .RData file.

Value

A list of:

n.samp	the total number of training samples
n.snp	the total number of candidate SNP predictors
sample.id	the sample IDs
snp.id	the SNP IDs
snp.position	SNP position in basepair
snp.allele	a vector of characters with the format of “A allele/B allele”
snp.allele.freq	the allele frequencies
hla.locus	the name of HLA locus
hla.allele	the HLA alleles used in the model
hla.freq	the HLA allele frequencies
assembly	the human genome reference, such like "hg19"
classifiers	a list of all classifiers (described as follows)
matching	matching proportion in the training set
appendix	platform – supported platform(s); information – other information, like training sets, authors; warning – any warning message

classifiers has the following components:

samp.num	the number of copies of samples in a bootstrap sample
haplos	a data.frame of haplotype frequencies
	freq – haplotype frequency
	hla – a HLA allele
	haplo – a SNP haplotype, with an entry value 0 standing for B (ZERO A allele), 1 for A (ONE A allele)
snpidx	the SNP indices used in this classifier
outofbag.acc	the out-of-bag accuracy of this classifier

Author(s)

Xiuwen Zheng

See Also

hlaAttrBagging, hlaParallelAttrBagging, hlaModelToObj, hlaModelFiles, hlaAttrBagClass

HIBAG documentation built on March 24, 2021, 6 p.m.