GRAB (version 0.2.4)

GRAB.SimuGMatFromGenoFile: Simulate genotype matrix from external genotype file

Description

Generates genotype matrices for families and unrelated subjects using haplotype data from existing genotype files. Primarily designed for rare variant analysis simulations.

Usage

GRAB.SimuGMatFromGenoFile(
  nFam,
  nSub,
  FamMode,
  GenoFile,
  GenoFileIndex = NULL,
  SampleIDs = NULL,
  control = NULL
)

Value

List containing:

GenoMat

Simulated genotype matrix (subjects × variants).

SubjIDs

Subject identifiers for simulated samples.

markerInfo

Variant information from input file.

Arguments

nFam

Number of families to simulate.

nSub

Number of unrelated subjects to simulate.

FamMode

Family structure: "4-members", "10-members", or "20-members". See Details for pedigree structures.

GenoFile

Path to genotype file (passed to GRAB.ReadGeno).

GenoFileIndex

Index file for genotype data (optional, for BGEN files).

SampleIDs

Vector of sample IDs to include (optional).

control

List of control parameters passed to GRAB.ReadGeno.

Details

This function supports both unrelated and related subjects. Founder genotypes are sampled from the input genotype file, and offspring genotypes are generated through Mendelian inheritance.

Note: When simulating related subjects, alleles are randomly assigned to haplotypes during the phasing process.

Family Structures:

• 4-members: Total subjects = nSub + 4×nFam. Structure: 1+2→3+4

• 10-members: Total subjects = nSub + 10×nFam. Structure: 1+2→5+6, 3+5→7+8, 4+6→9+10

• 20-members: Total subjects = nSub + 20×nFam. Structure: 1+2→9+10, 3+9→11+12, 4+10→13+14, 5+11→15+16, 6+12→17, 7+13→18, 8+14→19+20

Examples

nFam <- 50
nSub <- 500
FamMode <- "10-members"

# PLINK data format. Currently, this function does not support BGEN data format.
PLINKFile <- system.file("extdata", "example_n1000_m236.bed", package = "GRAB")
IDsToIncludeFile <- system.file("extdata", "example_n1000_m236.IDsToInclude", package = "GRAB")

GenoList <- GRAB.SimuGMatFromGenoFile(nFam, nSub, FamMode, PLINKFile,
  control = list(IDsToIncludeFile = IDsToIncludeFile)
)