# Convert genotype matrix to PLINK format files Converts a numeric genotype matrix to PLINK text files (PED and MAP format) for use with PLINK software and other genetic analysis tools. ```r GRAB.makePlink( GenoMat, OutputPrefix, A1 = "G", A2 = "A", CHR = NULL, BP = NULL, Pheno = NULL, Sex = NULL ) ``` ## Arguments - `GenoMat`: Numeric genotype matrix (n×m) with values 0, 1, 2, or -9. Rows = subjects, columns = markers. Row and column names are required. - `OutputPrefix`: Output file prefix including path (without extension). - `A1`: Allele 1 character, usually minor/ALT allele (default: "G"). - `A2`: Allele 2 character, usually major/REF allele (default: "A"). - `CHR`: Chromosome numbers for markers (default: all chromosome 1). - `BP`: Base positions for markers (default: 1:m). - `Pheno`: Phenotype values for subjects (default: all missing as -9). - `Sex`: Sex codes for subjects (default: all coded as 1). ## Returns Character message confirming file creation location. ## Details Genotype Encoding: * 0, 1, 2 → copies of minor allele * -9 → missing genotype (coded as "00" in PED) * A1="G", A2="A": 0→"GG", 1→"AG", 2→"AA", -9→"00" Output Files: * `.ped`: Pedigree file with genotype data * `.map`: Marker map file with positions Downstream Processing: ``` # Convert to binary format plink --file prefix --make-bed --out prefix # Convert to raw format plink --bfile prefix --recode A --out prefix_raw # Convert to BGEN format plink2 --bfile prefix --export bgen-1.2 bits=8 ref-first --out prefix_bgen # Create BGEN index bgenix -g prefix_bgen.bgen --index ``` ## Examples ```r ### Step 1: simulate a numeric genotype matrix n <- 1000 m <- 20 MAF <- 0.3 set.seed(123) GenoMat <- matrix(rbinom(n * m, 2, MAF), n, m) rownames(GenoMat) <- paste0("Subj-", 1:n) colnames(GenoMat) <- paste0("SNP-", 1:m) OutputDir <- tempdir() outputPrefix <- file.path(OutputDir, "simuPLINK") ### Step 2(a): make PLINK files without missing genotype GRAB.makePlink(GenoMat, outputPrefix) ### Step 2(b): make PLINK files with genotype missing rate of 0.1 indexMissing <- sample(n * m, 0.1 * n * m) GenoMat[indexMissing] <- -9 GRAB.makePlink(GenoMat, outputPrefix) ## The following are in shell environment # plink --file simuPLINK --make-bed --out simuPLINK # plink --bfile simuPLINK --recode A --out simuRAW # plink2 --bfile simuPLINK --export bgen-1.2 bits=8 ref-first --out simuBGEN # UK Biobank use 'ref-first' # bgenix -g simuBGEN.bgen --index ```

GRAB.makePlink function