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, covar, adjust.covar,
      chr, sum.scan = "yes", min.iter = 1,
      aggregate = TRUE, 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` | 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`.
`verbose` | Give verbose feedback if `TRUE`.

### Details

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.

### Value

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

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

[Package qtlbim version 1.6.5 Index]