qb.scanone {qtlbim}R Documentation

Genome Scan for Main Loci Involved in Phenotypic Trait

Description

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.

Usage

qb.scanone(qbObject, epistasis = TRUE, scan, type.scan, covar, adjust.covar,
  chr, sum.scan = "yes", min.iter = 1, aggregate = TRUE, smooth = 3,
  weight = c("sqrt","count","none"), split.chr,
  center.type = c("mode","mean","scan"), half = FALSE, verbose = FALSE, ...)

Arguments

qbObject An object of class qb.
epistasis If TRUE then information about epistasis is included.
scan Vector of diagnostics to scan (see below).
type.scan 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.
adjust.covar Adjustments to covariates. Default is NA, which adjusts by covariate mean values. Values are assumed to be in order of fixed 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.
smooth Degree of nearest neighbor smoothing to determine maxima.
weight Weights to use for nearest neighbor smoothing. sqrt is square root of count per locus. Used only if smooth > 0.
center.type Method to find QTL loci. See details.
split.chr Split summary by multiple QTL per chromosome (see details).
verbose Give verbose feedback if TRUE.
... Additional arguments mostly ignored.

Details

The type.scan 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.scan 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.

The "mode" and "mean" centering rely on the mode and mean, respectively, of the posterior; the "scan" centering uses the mode of the actual type used to create the qb.scanone object. The "scan" agrees with an scanone summary method for "pos" and "sum" columns. However, the mode for a "scan" could be in a region of low posterior mass and may not be reliable as such. Note that mean can be biased when there are linked loci. Only used in qb.scanone summary.

Evidence for linked loci leads to multiple summary lines per chromosome. Be default, a qbObject has inferred chromosome splits based on MCMC samples (see qb.split.chr). This is determined in a similar manner to qb.multloci. In particular, the arguments cutoff and nqtl documented in qb.multloci would adjust whether and how many linked loci may be considered. These apply across all chromosomes being summaried.

Value

Returns an object of class qb.scanone (a data frame) containing effects selected according to type.scan and scan.

Author(s)

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

References

http://www.qtlbim.org

See Also

summary.qb.scanone, plot.qb.scanone

Examples

data(qbExample)

temp <- qb.scanone(qbExample)
summary(temp)
plot(temp)

[Package qtlbim version 1.9.3 Index]