GRAB (version 0.2.3)

GRAB.SPACox: SPACox method in GRAB package

Description

SPACox method is an empirical approach to analyzing complex traits (including but not limited to time-to-event trait) for unrelated samples in a large-scale biobank.

Usage

GRAB.SPACox()

Value

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

Details

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

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

Examples

# Step 1: fit a null model
PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB")
PhenoData <- data.table::fread(PhenoFile, header = TRUE)
obj.SPACox <- GRAB.NullModel(
  survival::Surv(SurvTime, SurvEvent) ~ AGE + GENDER,
  data = PhenoData,
  subjData = IID,
  method = "SPACox",
  traitType = "time-to-event"
)

# Using model residuals performs exactly the same as the above. Note that
# confounding factors are still required in the right of the formula.
obj.coxph <- survival::coxph(
  survival::Surv(SurvTime, SurvEvent) ~ AGE + GENDER,
  data = PhenoData,
  x = TRUE
)

obj.SPACox <- GRAB.NullModel(
  obj.coxph$residuals ~ AGE + GENDER,
  data = PhenoData,
  subjData = IID,
  method = "SPACox",
  traitType = "Residual"
)

# Step 2: conduct score test
GenoFile <- system.file("extdata", "simuPLINK.bed", package = "GRAB")
OutputDir <- tempdir()
OutputFile <- file.path(OutputDir, "Results_SPACox.txt")
GRAB.Marker(
  objNull = obj.SPACox,
  GenoFile = GenoFile,
  OutputFile = OutputFile,
  control = list(outputColumns = "zScore")
)
data.table::fread(OutputFile)