read.bim {bim}R Documentation

Read samples from WinQTL output

Description

MCMC samples from WinQTL are organized into an object of class bim for diagnostic plots and analysis. This can be used to import MCMC samples from WinQTL or from an optional file saved by run.bmapqtl.

Usage

read.bim( dir, bimfile, nvalfile = "nval.dat", na.strings="." )

Arguments

dir directory containing files
bimfile name of MCMC sample file (currently with .z suffix)
nvalfile parameter file for Bmapqtl program (currently hard-wired)
na.strings missing value code

Details

Bmapqtl used to operate as a separate external command, but was recently incorporated as a C dynamic library. However, read.bim is still useful for output from WinQTL. For information on WinQTL visit http://statgen.ncsu.edu/qtlcart.

Value

An object of class `bim', which is a list with components

bmapqtl parameter settings for Bmapqtl run
burnin burnin sequence data frame, containing niter = iteration number, nqtl = number of QTL, LOD = LOD score based on simulated QTL genotypes, mean = grand mean of phenotype, envvar = environmental variance, addvar = additive variance, domvar = dominance variance (if included), and herit = heritability.
iter MCMC iteration summary data frame, with same elements as burnin.
loci data frame with MCMC estimates across loci by iteration, containing niter = iteration number, nqtl = number of QTL, chrom = chromosome number, locus = locus position in centi-Morgans, add = additive effect, dom = dominance effect (if included).

Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

See Also

plot.bim,run.bmapqtl,read.bmapqtl

Examples

## Not run: verngeo.bim <- read.bim( ".", "verngeo.z" )

[Package bim version 1.01-1 Index]