qb.scanone {qtlbim} | R Documentation |
This method extracts iteration diagnostics and mainloci from the
qb
object and returns a data frame (of class qb.scanone
)
containing information on environmental variance, explained variance
components, non-epistatic variance components.
qb.scanone(qbObject, epistasis = TRUE, scan, type, covar, chr, sum.scan = "yes", min.iter = 1, aggregate = TRUE, half = FALSE, verbose = FALSE)
qbObject |
An object of class qb . |
epistasis |
If TRUE then information about
epistasis is included. |
scan |
Vector of diagnostics to scan (see below). |
type |
Type of scan; default is "heritability" (see below). |
covar |
Covariate(s) to include; default is seq(nfixcov)
where nfixcov is taken from qb.data . Set to 0
to exclude any covariates. |
chr |
Chromosomes to subset on if not NULL . |
sum.scan |
Sum over scan diagnostics if "yes" or "only";
only report sum if "only". |
min.iter |
Include only samples at loci if minimum number of
iterations is at least min.iter ; default is to include all
(min.iter = 1). |
aggregate |
Aggregate effects into main, epis, gbye if TRUE . |
half |
Cut epistatic effects in half if TRUE . |
verbose |
Give verbose feedback if TRUE . |
The type
specifies what type of scan is performed. Scan produces
marginal estimates of diagnostics at each potential loci across the
genome. That is, values are adjusted for other possible QTL simply by
taking the marginal average over MCMC samples. Choices of type
are
"heritability", "LPD", "LR", "deviance", "detection", "variance",
"estimate", "cellmean", "count", "log10", "posterior", "logposterior"
(i.e. log10(posterior)), "BF", "2logBF" (i.e. 2*ln(BF)), and "nqtl"
(number of linked QTL). Default is "LPD".
Type "heritability" is actually R-squared at this point, not the theoretical
heritability.
Types "LPD", "LR" and "deviance" are all proportional to each other in
the usual sense; "LPD" is computed to agree with lod
from
scanone
if models were restricted to one QTL and missing
genotypes are imputed. Detection is the marginal posterior probability of
detectio of a QTL at a locus.
Types "variance" and "estimate" yield, respectively, the marginal variance
components and the marginal parameter estimates at each loci. Type
"cellmean" gives marginal estimates for A, H, B genotypes (these are
single character codes for AA, AB, BB, respectively). The remaining
count types provide diagnostics. Types "count" and "log10" report on
number of MCMC samples in raw or logged scale. Type
"posterior" ("logposterior") yields the marginal (log) posterior
probability. Type "BF" ("2logBF") gives the marginal
Bayes factor per loci; both are proportional to "count". Type "nqtl"
gives the average number of linked loci, which can be useful in sorting
out multiple linked loci.
The scan
specifies the model effects to include for all types
except the counts. Aggregated effects (default except for type
"cellmean") are "main", "epistasis" and "GxE" (genotype by
environment). Individual model effects can be requested
as "add", "dom", "aa", "ad", "da", "dd". In addition, GxE terms, if
present are included automatically if covar
is not 0. For type
"estimate", main effects for "add" and "dom" are adjusted for any
covariate GxE effects. The sum.scan
is used for all types but the
counts to get a summary across scan
effects.
Returns an object of class qb.scanone
(a data frame) containing
effects selected according to type
and scan
.
Brian S. Yandell, yandell@stat.wisc.edu
summary.qb.scanone
, plot.qb.scanone
temp <- qb.scanone(qbExample) summary(temp) plot(temp, chr = c(1,3,5,7,10,12,19))