GRAB (version 0.2.3)

GRAB.SPAmix: SPAmix method in GRAB package

Description

SPAmix 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. SPAmix extend SPACox to support an admixture population or multiple populations.

Usage

GRAB.SPAmix()

Value

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

Details

For SPAmix, the confounding factors of SNP-derived PCs are required and should be specified in control.

Examples

# Step 1: fit a null model
PhenoFile <- system.file("extdata", "simuPHENO.txt", package = "GRAB")
PhenoData <- data.table::fread(PhenoFile, header = TRUE)

# Users can directly specify a time-to-event trait to analyze
obj.SPAmix <- GRAB.NullModel(
  survival::Surv(SurvTime, SurvEvent) ~ AGE + GENDER + PC1 + PC2,
  data = PhenoData,
  subjData = IID,
  method = "SPAmix",
  traitType = "time-to-event",
  control = list(PC_columns = "PC1,PC2")
)

# 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 + PC1 + PC2,
  data = PhenoData
)

obj.SPAmix <- GRAB.NullModel(
  obj.coxph$residuals ~ AGE + GENDER + PC1 + PC2,
  data = PhenoData,
  subjData = IID,
  method = "SPAmix",
  traitType = "Residual",
  control = list(PC_columns = "PC1,PC2")
)

# SPAmix also supports multiple residuals as below
obj.coxph <- survival::coxph(
  survival::Surv(SurvTime, SurvEvent) ~ AGE + GENDER + PC1 + PC2, 
  data = PhenoData
)
obj.lm <- lm(QuantPheno ~ AGE + GENDER + PC1 + PC2, data = PhenoData)

obj.SPAmix <- GRAB.NullModel(
  obj.coxph$residuals + obj.lm$residuals ~ AGE + GENDER + PC1 + PC2,
  data = PhenoData,
  subjData = IID,
  method = "SPAmix",
  traitType = "Residual",
  control = list(PC_columns = "PC1,PC2")
)

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