makePlinkInputFile: Make PLINK input files
In HapEstXXR: Multi-Locus Stepwise Regression

Description Usage Arguments Details Value Author(s) References See Also

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

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

`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

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

no return values.

Sven Knueppel

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)

makeHaploviewInputFile, allele1to2

HapEstXXR documentation built on May 1, 2019, 10:54 p.m.