burdenTest: Compute weighted burden test

In bhattacharya-a-bt/MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies

Compute weighted burden test

Description

The function takes in a gene expression model in MOSTWAS form and GWAS summary statistics and carries out the weighted burden Z-test for a trait

Usage

burdenTest(
  wgt,
  snps,
  sumStats,
  snpAnnot = NULL,
  onlyCis = F,
  Z = NULL,
  beta = NULL,
  se = NULL,
  chr,
  pos,
  ref,
  pval,
  R2cutoff,
  alpha,
  locChrom,
  nperms = 1000
)

Arguments

wgt	character, name of expression model .RData file
snps	data.frame, reference panel SNPs
sumStats	data frame, GWAS summary statistics
snpAnnot	data.frame, SNP REF/ALT annotations
onlyCis	logical, T/F to consider only cis-component
beta	character, colnames in sumStats that keeps the effect sizes
se	character, colnames in sumStats that keeps the standard errors
chr	character, colnames in sumStats that keeps the chromosome
pos	character, colnames in sumStats that keeps the position
ref	character, colnames in sumStats that keeps the reference allele
R2cutoff	numeric, predictive R2 cutoff
alpha	numeric, P-value threshold for permutation testing
nperms	numeric, number of permutations

Value

list of results for burden and permutation tests

bhattacharya-a-bt/MOSTWAS documentation built on April 6, 2023, 12:20 a.m.