rareMETALS.range.group.core: 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.range.group.core(score.stat.file, cov.file, range, range.name,
  test = "GRANVIL", refaltList, maf.cutoff = 1,
  alternative = c("two.sided", "greater", "less"), out.digits = 4,
  callrate.cutoff = 0, hwe.cutoff = 0, max.VT = NULL,
  correctFlip = TRUE, analyzeRefAltListOnly = TRUE)

Arguments

score.stat.file	files of score statistics
cov.file	Covariance matrix files
range	tabix range for each gene/region; Tabix range needs to be in the format of "1:123-1234". Quotation marks are necessary.
range.name	The name of the range,e.g. gene names can be used;
test	rare variant tests to be used
refaltList	A list of reference, alternative allele, a vector of alternative allele frequencies; Specifically, the list should consist of
maf.cutoff	MAF cutoff used to analyze variants; Default value is 1, i.e. no cutoffs are applied. MAFs are based upon the sample MAFs.
alternative	alternative hypothesis to be specified; Only applicable to GRANVIL test;
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; For small p-values, the calculation of VT p-values can be very slow. 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.