pvalueCorrection: Function that correct P value for alleles or haplotypes or...

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

Description

Function that correct P value for alleles or haplotypes or Amino Acids. Propose 2 differents methods: bonferroni with allele's regression result or Permutation by redoing regression over 1000 times or different number of loop.

Usage

pvalueCorrection(allele = NULL, haplo = NULL, AA = NULL,
  KIR = NULL, HLAC = NULL, alleleRegResult = NULL,
  haploRegResult = NULL, AARegResult = NULL, pcaFile = NULL,
  statut = NULL, correction = "bonferroni")

Arguments

allele	Imputation's result file with 14 colunms : subjectID, Disease, PC1, PC2, prob, A, A, B, B, C, C, DRB1, DRB1, DQB1, DQB1 ("," separator between fields)
haplo	Haplotypes file with at least these columns : subjectID, A-B-C-DR-DQ-1, freq1, A-B-C-DR-DQ-2, freq2, PostP ("," separator between fields)
AA	Amino-Acid File from easy-hla
KIR	KIR ligand's file from easy-hla
HLAC	HLAC expression as provided by easy-hla
alleleRegResult	result file of Regression on allele : function allelicReg
haploRegResult	result file of Regression on haplotypes : function haploReg
AARegResult	result file of Regression on AA : function aaReg
pcaFile	FIle with sample id and two principal components of PCA
statut	File with sample id and disease statut (coded 0 1)
correction	Method to correct P value and display a line of the new critical P value.

Value

Return a list with the new critical P value for each level of analysis: seuilAllele, seuilHaplo and seuilAA

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