Train a local-only model for a phenotype — trainSNPPheno • MOSTWAS

The function runs FUSION-type local-only modeling for a phenotype

trainSNPPheno(
  pheno,
  snpCur,
  snpList,
  thisSNP,
  fileName,
  prune = T,
  windowSize = 50,
  numSNPShift = 5,
  ldThresh = 0.5,
  verbose = T,
  snpAnnot = NULL
)

Arguments

pheno	vector, phenotypes
snpCur	matrix, SNP dosages
snpList	vector, vector of SNP identifiers
thisSNP	data.frame, SNP locations
fileName	character, prefix for LDprune
prune	logical, T/F to LD prune
windowSize	numeric, PLINK LD prune window size
numSNPShift	integer, PLINK LD shifting interval
ldThresh	numeric, LD threshold
verbose	logical, T/F for verbosity
snpAnnot	data.frame, SNP annotations

Value

list with TME and P-value