binary.rareMETALS.single.group: Single variant meta-analysis

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

Description

Single variant meta-analysis

Usage

binary.rareMETALS.single.group(score.stat.file, cov.file, range, refaltList,
  alternative = c("two.sided", "greater", "less"), callrate.cutoff = 0,
  hwe.cutoff = 0, correctFlip = TRUE, analyzeRefAltListOnly = TRUE)

Arguments

score.stat.file	files of score statistics
cov.file	covariance matrix files
range	tabix range of variants to be analyzed
refaltList	A list of reference alternative and positions of variants to be analyzed; Each variant in the dataset will be match against ref/alt alleles specified in refaltList; Only variants with matched ref and alt alleles can be included; we also need AF and af.diff.max to determine if the flips are due to strand issues or due to ref/alt alleles flips;
alternative	alternative hypothesis to be specified
callrate.cutoff	Cutoffs of call rate, lower than which will NOT be analyzed (labelled as missing)
hwe.cutoff	Cutoffs of HWE p-values
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;
refaltList	A list that contains pos, ref and alt for calibrating variant sites to have the right ref and alt alleles;

Value

a list consisting of results

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