qtl.outbred-package: Interface for Genotype Probabilities of Outbred Intercross

In qtl.outbred: Interface for Genotype Probabilities from Outbred Intercross

Description

The package calculates and imports genotype probabilities from outbred intercross designs into an R object. This allows fast scans for main effect QTL and two way interactions. Using this interface, most functions in package qtl can be used for outbred designs.

Details

Package:	qtl.outbred
Type:	Package
Version:	2013.05.03
Date:	2013-05-03
License:	GPL
LazyLoad:	yes
Depends:	qtl

Author(s)

Ronnie Nelson and Xia Shen

Maintainer: Xia Shen <[e-mail]>

See Also

impo.prob, calc.prob

Examples

## Not run: 
file <- paste(R.home(), '/library/qtl.outbred/example_data.csv', sep = '')
data <- read.cross('csv', file = file, genotypes = c('AA', 'AB', 'BB'))
path <- paste(R.home(), '/library/qtl.outbred/', sep = '')
outbred.data <- impo.prob(cross.data = data, path = path, stepsize = 5)

# ----- QTL scan using Haley-Knott regression and plotting
hk.model <- scanone(outbred.data, method = 'hk', pheno.col = 2) 
plot(hk.model)

## End(Not run)

qtl.outbred documentation built on May 2, 2019, 5:56 p.m.