hlaHaplotypeAnalysis: Analysis of HLA haplotypes and many phenotypes

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

Description

Analysis of HLA haplotypes and many phenotypes

Usage

hlaHaplotypeAnalysis(haploDataPath, statut, phenoPath = NULL,
  pcaPath = NULL, covarPath = NULL, outputFolder, outputFile,
  type = "pheno")

Arguments

haploDataPath	Hla haplotypes file pathways
statut	file conaining subject ID and Disease statut
phenoPath	phenotypes file with different trait names in columns
pcaPath	pca result for PC1 and PC2
covarPath	must contains SubjectID followed by covariables
outputFolder	folder where to save the result
outputFile	Name for the result csv file with columns: subjectID Disease PC1 PC2 A A B B C C DRB1 DRB1 DQB1 DQB1
type	etiher "disease" for analysis in case/control or "pheno" for analysis with an quantitative phenotype

Value

Linear Regression result with the phenotypes as covariates

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