rareGWAMA.single: single variant meta-analysis integrating imputation quality;

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

Description

single variant meta-analysis integrating imputation quality;

Usage

rareGWAMA.single(score.stat.file, imp.qual.file = NULL, tabix.range,
  alternative = "two.sided", col.impqual = 5, impQual.lb = 0.7,
  impQualWeight = FALSE, rmMultiAllelicSite = FALSE, gc = FALSE, ...)

Arguments

score.stat.file	the file names of score statistic files;
imp.qual.file	the file names of imputation quality;
tabix.range	the tabix range. IT must be in quote and provided as a string;
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.single(score.stat.file = study.vec, imp.qual.file = r2.vec ,"1:10177-57200", 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.