GRAB (version 0.2.3)

GRAB.POLMM: POLMM method in GRAB package

Description

POLMM method is to analyze ordinal categorical data for related samples in a large-scale biobank.

Usage

GRAB.POLMM()

Value

No return value, called for side effects (prints information about the POLMM method to the console).

Details

Please check ?GRAB.control for the generic list of control in GRAB.NullModel() and GRAB.Marker().

Additional list of control in GRAB.NullModel() function Additional list of control in GRAB.Marker() function Additional list of control in GRAB.Region() function

Examples

### First, read phenotype data and convert to a factor
PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB")
PhenoData <- data.table::fread(PhenoFile, header = TRUE)
PhenoData$OrdinalPheno <- factor(PhenoData$OrdinalPheno, levels = c(0, 1, 2))

### Step 1: Fit a null model
# If SparseGRMFile is provided, the sparse GRM will be used in model fitting.
# If SparseGRMFile isn't provided, GRAB.NullModel() will calculate dense GRM from GenoFile.
SparseGRMFile <- system.file("extdata", "SparseGRM.txt", package = "GRAB")
GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")

obj.POLMM <- GRAB.NullModel(
  formula = OrdinalPheno ~ AGE + GENDER,
  data = PhenoData,
  subjData = PhenoData$IID,
  method = "POLMM",
  traitType = "ordinal",
  GenoFile = GenoFile,
  SparseGRMFile = SparseGRMFile,
  control = list(
    showInfo = FALSE,
    LOCO = FALSE,
    tolTau = 0.2,
    tolBeta = 0.1
  )
)

### Step 2(a): Single-variant tests using POLMM
GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
OutputFile <- file.path(tempdir(), "simuMarkerOutput.txt")

GRAB.Marker(
  objNull = obj.POLMM,
  GenoFile = GenoFile,
  OutputFile = OutputFile
)

data.table::fread(OutputFile)

### Step 2(b): Set-based tests using POLMM-GENE
GenoFile <- system.file("extdata", "simuPLINK_RV.bed", package = "GRAB")
OutputFile <- file.path(tempdir(), "simuRegionOutput.txt")
GroupFile <- system.file("extdata", "simuPLINK_RV.group", package = "GRAB")
SparseGRMFile <- system.file("extdata", "SparseGRM.txt", package = "GRAB")

GRAB.Region(
  objNull = obj.POLMM,
  GenoFile = GenoFile,
  GenoFileIndex = NULL,
  OutputFile = OutputFile,
  OutputFileIndex = NULL,
  GroupFile = GroupFile,
  SparseGRMFile = SparseGRMFile,
  MaxMAFVec = "0.01,0.005"
)

data.table::fread(OutputFile)