hlaImputation: Impute HLA allele by using HiBAG package

In benabidlina/HLAfix: HLA Analysis Pipeline for large-scale Association Studies

Description

Impute HLA allele by using HiBAG package

Usage

hlaImputation(bedFile, bimFile, famFile, hlaLoci = c("A", "B", "C",
  "DRB1", "DQB1"), trainingModel = NULL, pcaFile, outputFolder,
  probThreshold = 0.5)

Arguments

bedFile	.bed file containing the packed binary SNP genotype data
bimFile	.bim file containingthe SNP descriptions
famFile	.fam file containing subject (and, possibly, family) identifiers. This is basically a tab-delimited "pedfile"
hlaLoci	vector of HLA loci, by default it is: A B C DPR1
trainingModel	Model for hibag training. Download pre-fit Model https://github.com/zhengxwen/HIBAG
pcaFile	FIle with two principal components of PCA
outputFolder	folder where to save the result
probThreshold	Threshold of Postprob from Hibag to keep. By default 0.5

Value

All HLA alleles with imputation probabilities

benabidlina/HLAfix documentation built on Aug. 20, 2021, 11:53 p.m.