rareGWAMA.cond.single: conditional analysis for single variant association test;

In dajiangliu/rareGWAMA: Meta-Analysis of Gene-level Rare Variant Association Test in Whole Genome Datasets

Description

conditional analysis for single variant association test;

Usage

rareGWAMA.cond.single(score.stat.file, imp.qual.file = NULL, vcf.ref.file,
  candidateVar, knownVar, alternative = "two.sided", ...)

Arguments

score.stat.file	the file names of score statistic files;
imp.qual.file	the file names of imputation quality;
vcf.ref.file	the file names of the reference panel file;
candidateVar	the tabix range;
knownVar	known variant;
alternative	The alternative hypothesis. Default is two.sided;
col.impqual	The column number for the imputation quality score;
impQual.lb	The lower bound for the imputation quality. Variants with imputaiton quality less than impQual.lb will be labelled as missing;
impQualWeight	Using imputation quality as weight
rmMultiAllelicSite	Default is TRUE. Multi-allelic sites will be removed from the analyses if set TRUE, and a variable posMulti will be output; The variant site with multiple alleles can be analyzed using rareGWAMA.single.multiAllele function;

Value

A list of analysis results;

Examples

study.vec <- c("rareGWAMA/inst/extdata/study1.gz", "rareGWAMA/inst/extdata/study1.R2.gz", "rareGWAMA/inst/extdata/study3.gz");
r2.vec <- c("rareGWAMA/inst/extdata/study1.R2.gz", "rareGWAMA/inst/extdata/study2.R2.gz", "rareGWAMA/inst/extdata/study3.R2.gz");
res <- rareGWAMA.cond.single(score.stat.file= study.vec, imp.qual.file = r2.vec, vcf.ref.file = "rareGWAMA/inst/extdata/1kg_fra_chr1.vcf.gz", "1:10177", "1:57200", 
                             alternative="two.sided",col.impqual=5,impQual.lb=0,impQualWeight=FALSE, weight="Npq+impQ",gc=FALSE, 
                             rmMultiAllelicSite=TRUE);
head(res$res.formatted);

dajiangliu/rareGWAMA documentation built on Sept. 13, 2019, 9:14 a.m.