HapEstXXR (version 0.1-8)

makeHaploviewInputFile: Make Haploview input files

Description

Create two data sets (*.ped and *.info) as input files for Haploview

Usage

makeHaploviewInputFile(famid, patid, fid, mid, sex, aff, geno, marker.name,  marker.position, haploview.pedfile, haploview.infofile)

Arguments

famid

Family ID

patid

Individual ID

fid

Paternal ID

mid

Maternal ID

sex

1=male, 2=female, other=unknown

aff

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

geno

(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.

marker.name

marker name

marker.position

marker position

haploview.pedfile

specify target of linkage file

haploview.infofile

specify target of marker Information file

Value

no return values.

Details

This function provides only limited options for creating Haploview input files. For more details see Haploview/URL: http://www.broadinstitute.org/mpg/haploview.

References

Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization

of LD and haplotype maps. Bioinformatics. 2005; 21(2):263-265. [PubMed ID: 15297300]

Haploview/URL: http://www.broadinstitute.org/mpg/haploview

See Also

makePlinkInputFile, allele1to2