Data can be loaded in haploview format (linkage format) with columns of family,
individual, father, mother, gender (1 = male, 2 = male), affected status
(0 = unkown, 1 = unaffected, 2 = affected), and genotypes(2 columns alleles).
Usage
read.haploview(ped.file, map.file)
Arguments
ped.file
Localizion of a pedigree file.
map.file
Localizion of a marker information file.
Value
famid
family identifier
patid
individual identifier
dad
father identifier (0=unkown)
mom
mother identifier (0=unkown)
sex
sex (0=unkown,1=male,2=female)
genotypes
(n,m)-matrix; n=No. of individuals; m=No. of SNPs; 1-column allele dosis
trait
phenotype values
marker.names
marker.names
marker.position
Base-pair position on chromosome (base pair units)
Details
The marker information file should contain in the first column the marker name
and the second column the physical position on the chromosome.
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]