HapEstXXR (version 0.1-8)

makePlinkInputFile: Make PLINK input files

Description

Create two data sets (*.ped and *.map) as input files for PLINK

Usage

makePlinkInputFile(famid, patid, fid, mid, sex, trait, CHR, SNP, POS, geno.matrix, linkage.file, map.file, cov.file)

Arguments

famid

Family ID

patid

Individual ID

fid

Paternal ID

mid

Maternal ID

sex

1=male, 2=female, other=unknown

trait

disease phenotype (1=unaff, 2=aff, -9 or 0=missing/unkown)

CHR

chromosome

SNP

marker name

POS

marker position

geno.matrix

(n,m) genotype matrix (n=number of individuals, m=number of marker, 1-column for every marker, R-code: 1 = 1/1, 3 = 1/2, 2 = 2/2); All markers should be biallelic.

linkage.file

specify target of linkage file

map.file

specify target of map file

cov.file

specify target of cov file

Value

no return values.

Details

This function provides only limited options for creating PLINK input files. For more details see PLINK/URL: http://pngu.mgh.harvard.edu/~purcell/plink/.

References

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81. (PLINK/URL: http://pngu.mgh.harvard.edu/~purcell/plink)

See Also

makeHaploviewInputFile, allele1to2