read.bim {bim} | R Documentation |
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.
read.bim( dir, bimfile, nvalfile = "nval.dat", na.strings="." )
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 |
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.
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). |
Brian S. Yandell, yandell@stat.wisc.edu
plot.bim
,run.bmapqtl
,read.bmapqtl
## Not run: verngeo.bim <- read.bim( ".", "verngeo.z" )