read.haploview: Read a haploview dataset

In HapEstXXR: Multi-Locus Stepwise Regression

Description

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.

Details

The marker information file should contain in the first column the marker name and the second column the physical position on the chromosome.

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)

Author(s)

Sven Knueppel

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

read.data

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