GRAB (version 0.2.2)

GRAB.SimuGMatFromGenoFile: GRAB: simulate genotype matrix based on family structure

Description

Simulate genotype matrix based on family structure using haplotype information from genotype files. This function is mainly to simulate genotype data for rare variants analysis. NOTE: if simulating related subjects, the genotype of two allele will be assigned to two haplotypes of one allele randomly.

Usage

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

Value

a genotype matrix of genotype data

Arguments

nFam

number of families in simulation

nSub

number of unrelated subjects in simulation

FamMode

"4-members", "10-members", or "20-members". Check Details section for more details.

GenoFile

this parameter is passed to GRAB.ReadGeno to read in genotype data.

GenoFileIndex

this parameter is passed to GRAB.ReadGeno to read in genotype data.

SampleIDs

this parameter is passed to GRAB.ReadGeno to read in genotype data.

control

this parameter is passed to GRAB.ReadGeno to read in genotype data.

Details

Currently, function GRAB.SimuGMatFromGenoFile supports both unrelated and related subjects. Genotype data of founders is from GenoFile and GenoFileIndex.

If FamMode = "4-members"

Total number of subjects is nSub + 4 * nFam. Each family includes 4 members with the family structure as below: 1+2->3+4.

If FamMode = "10-members"

Total number of subjects is nSub + 10 * nFam. Each family includes 10 members with the family structure as below: 1+2->5+6, 3+5->7+8, 4+6->9+10.

If FamMode = "20-members"

Total number of subjects is nSub + 20 * nFam. Each family includes 20 members with the family structure as below: 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)
)