rareMETALS.estimatePVE: Estimate the variance explained for a list of variants...

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

Description

Estimate the variance explained for a list of variants (possibly in LD);

Usage

rareMETALS.estimatePVE(score.stat.file, cov.file, range, range.name, refaltList,
  maf.cutoff, out.digits, callrate.cutoff, hwe.cutoff, correctFlip = TRUE,
  lambda = 0)

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;
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.
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
correctFlip	Correct for flipped sites for score statistics and their covariance matrices
lambda	Tuning parameter to the variant the variance correlation matrix to avoid near singular LD matrix; Assume the orignal LD matrix is R2, R2.adj=R2+lambda*Id;

Value

a list consisting of results;

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