conditional.rareMETALS.single.group.core: 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.group.core(candidate.variant, score.stat.file,
  cov.file, known.variant.vec, refaltList, maf.cutoff,
  alternative = c("two.sided", "greater", "less"), out.digits = 4,
  callrate.cutoff = 0, hwe.cutoff = 0, correctFlip = TRUE,
  knownCoding = "identity", impMissing = FALSE)

Arguments

candidate.variant	Candidate variant position;
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");
refaltList	A list of ref, alt alleles, as well as variant frequencies, whether it needs to check AF as for flipping alleles;
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
knownCoding	knownCoding option allows users to specify if a linear transformation needs to be applied known variants. Possible choices for knownCoding option include identical, burden, randomm-eff.
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.