conditional.rareMETALS.range.group: Perform conditional analysis for gene-level tests and...

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

Description

Perform conditional analysis for gene-level tests and correcting for allele flips with

Usage

conditional.rareMETALS.range.group(range.name = NULL, score.stat.file,
  cov.file, candidate.variant.vec, known.variant.vec, test = "GRANVIL",
  maf.cutoff, alternative = c("two.sided", "greater", "less"), refaltList,
  out.digits = 4, callrate.cutoff = 0, hwe.cutoff = 0, max.VT = NULL,
  correctFlip = TRUE, analyzeRefAltListOnly = TRUE)

Arguments

range.name	name of the range to be analyzed (for example, it can be a gene name e.g. APOE)
score.stat.file	files of score statistics
cov.file	covariance matrix files
candidate.variant.vec	Vectors of candidate variants: e.g. c("1:123","1:1234"). The quotation is necessary!!
known.variant.vec	Vectors of known variants: e.g. c("1:123","1:1234"). The quotation is necessary!!
test	test of rare variant tests
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
max.VT	The maximum number of thresholds used in VT; Setting max.VT to 10 can improve the speed for calculation without affecting the power too much. The default parameter is NULL, which does not set upper limit on the number of variable frequency threhsold.
correctFlip	Correcting for flipped alleles; Default is TRUE; If FALSE, studies with incorrect REF/ALT alleles will be labelled as missing, and dropped from meta-analyses
analyzeRefAltListOnly	Only analyze variants that are included in the refaltList; Default is TRUE; If FALSE, variant sites in the dataset but not specified in the refaltList will be labelled as missing and dropped from studies;
ix.gold	Index of the gold standard population: Used for flipping alleles

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