estimateHeritability: Estimate germline heritability of a biomarker

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

Estimate germline heritability of a biomarker

Description

The function invokves GCTA in the system and estimates the germline heritability of a biomarker given cis-regions around the biomarker and any associated mediators of interest.

Usage

estimateHeritability(
  biomInt,
  snps,
  pheno,
  snpLocs,
  mediator,
  medLocs,
  covariates,
  fileName,
  dimNumeric,
  numMed = 5,
  cisDist = 5e+05,
  needMed = T,
  prune = F,
  medList,
  verbose = F,
  windowSize,
  numSNPShift,
  ldThresh,
  ldScrRegion = 200,
  LDMS = F,
  supplySNP = F,
  snpAnnot = NULL
)

Arguments

biomInt	character, identifier for biomarker of interest
snps	data frame, SNP dosages
snpLocs	data frame, MatrixEQTL locations for SNPs
mediator	data frame, mediator intensities
medLocs	data frame, MatrixEQTL locations for mediators
covariates	data frame, covariates
fileName	character, throw away name for PLINK files
dimNumeric	integer, number of continuous covariates
numMed	integer, maximum number of mediators to find
cisDist	numeric, base pair window of cis definition
needMed	logical, T/F if the biomarker of interest has associated mediators
medList	character vector, vector of mediator names
verbose	logical, T/F for detailed output
windowSize	integer, window size for PLINK pruning
numSNPShift	integer, shifting window from PLINK pruning
ldThresh	numeric, maximum threshold for linkage disequilibrium
ldScrRegion	numeric, number of SNPs per bin in GCTA-LDMS
LDMS	logical, T/F to run GCTA-LDMS
supplySNP	logical, T/F to run GCTA on the full provided snps

Value

heritability estimate and associated LRT P-value

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