hlaAlleleAnalysis: Analysis of HLA allele and many variate phenotypes

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

Description

Take a file containing 14 colunms as input subjectID Disease PC1 PC2 A A B B C C DRB1 DRB1 DQB1 DQB1 ("," separator between fields) AND a file with differents phenotypes : subjectID traitName1 traitName2 traitName3 traitName4 traitName5

Usage

hlaAlleleAnalysis(dataPath, phenoPath = NULL, covarPath = NULL,
  outputFolder, outputFile, type = "pheno")

Arguments

dataPath	Hla allele file pathways. Contains with columns: subjectID Disease PC1 PC2 A A B B C C DRB1 DRB1 DQB1 DQB1.
phenoPath	phenotypes file with different trait names in columns
covarPath	must contains SubjectID followed by covariables
outputFolder	folder where to save the result
outputFile	Name for the result csv file
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.