scantwo: Genome Scan for Pairs of Loci Involved in Phenotypic Trait

In byandell/qtlbim: QTL Bayesian Interval Mapping

Description

This method extracts iteration diagnostics and pair loci from the qb object and returns a data frame (of class qb.scanone) containing information on environmental variance, explained variance components, epistatic and non-epistatic variance components.

Usage

qb.scantwo(qbObject, epistasis = TRUE, scan, type.scan,
  upper.scan = "epistasis", lower.scan = "full", covar,
  adjust.covar, chr, min.iter = 1, verbose = FALSE, ...)

Arguments

qbObject	An object of class qb.
epistasis	If TRUE information on epistasis is included in the return value.
scan	List of diagnostics to scan (see below).
type.scan	Vector of two scan types; default is "heritability" (see below).
upper.scan	Vector of diagnostics to scan for upper triangle (see below).
lower.scan	Vector of diagnostics to scan for lower triangle (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.
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).
verbose	Give verbose feedback if TRUE.
...	Additional arguments mostly ignored.

Details

The scan and type.scan are similar to those used in qb.scanone. However, here scan is a list and type.scan is a vector, each with elements "lower" and "upper". You can either specify scan as a list, or profide upper.scan and lower.scan separately.

The scan defaults for types other than counts to list(upper = "epistasis", lower = "full"); you can modify the list scan or the separate options upper.scan and lower.scan. The string "epistasis" is short-hand for the epistatic effects, c("aa", "ad", "da", "dd"). The string "full" is shorthand for the epistatics effects plus main effects, c("add", "dom"), plus any GxE terms.

The type.scan defaults to c(upper = "LPD", lower = "LPD"). See qb.scanone for the range of possible types. Mostly the 2-D version of type.scan provides marginal summaries for pairs of loci. However, for type "nqtl", the marginal summaries involving main effects (e.g. with scan values "full" or "main" or "add" or "dom") show, for each pair of chromosomes, the average number of QTL at both chromosomes.

Value

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

Author(s)

Brian S. Yandell, [e-mail]

References

http://www.qtlbim.org

See Also

plot.qb.scanone

Examples

data(qbExample)

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

byandell/qtlbim documentation built on Dec. 19, 2021, 12:47 p.m.