Train a local-only model for a phenotype

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