conditional.rareMETALS.single: Perform conditional analysis for single variant tests

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

Description

Perform conditional analysis for single variant tests

Usage

conditional.rareMETALS.single(candidate.variant.vec, score.stat.file, cov.file,
  known.variant.vec, maf.cutoff, no.boot = 10000,
  alternative = c("two.sided", "greater", "less"), ix.gold = 1,
  out.digits = 4, callrate.cutoff = 0, hwe.cutoff = 0,
  p.value.known.variant.vec = NA, anno.known.variant.vec = NA,
  anno.candidate.variant.vec = NA, knownCoding = "identity")

Arguments

score.stat.file	files of score statistics
cov.file	covariance matrix files
known.variant.vec	range of candidate variant, expressed in a vector, e.g. c("1:12345","1:234567");
maf.cutoff	Cutoffs of MAF used for determining rare variants
alternative	Alternative hypothesis to be tested
out.digits	The number of digits used in the output
callrate.cutoff	Cutoff of call rates. Sites with callrates lower than the cutoff will be labeled as missing
hwe.cutoff	Cutoff of HWE p-values. Sites with HWE pvalues lower than the cutoff will be labeled as missing
candidate.variant	name of the range to be analyzed (for example, it can be a gene name e.g. APOE)
known.variant.range	range of known variant, expressed in tabix format, e.g. c("1:123456","1:2345678");
test	test of rare variant tests

Value

return a list of meta-analysis results

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