rareMETALS.gene.group: Meta-analysis of gene-level tests by range;

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

Description

Meta-analysis of gene-level tests by range;

Usage

rareMETALS.gene.group(score.stat.file, cov.file, range, range.name,
  test = "GRANVIL", refaltList, maf.cutoff = 1, no.boot = 10000,
  alternative = c("two.sided", "greater", "less"), alpha = 0.05,
  ix.gold = 1, out.digits = 4, callrate.cutoff = 0, hwe.cutoff = 0,
  max.VT = NULL)

Arguments

score.stat.file	files of score statistics
cov.file	covariance matrix files
range	tabix range for each gene/region
range.name	The name of the range,e.g. gene names can be used
test	rare variant tests to be used
refaltList	List of reference, alternative and variant positions;
maf.cutoff	MAF cutoff used to analyze variants
no.boot	Number of bootstraps to be used. No need if asymptotics are used
alternative	alternative hypothesis to be specified
alpha	Significance threshold to determine the number of resampling. Set to 0 if analytic p-values are calculated.
ix.gold	Gold standard population to align reference allele to
out.digits	Number of digits used in the output
callrate.cutoff	Cutoffs of call rate, lower than which will NOT be analyzed (labelled as missing)
hwe.cutoff	Cutoffs of HWE p-values
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.

Value

a list consisting of results

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