qb.scantwo {qtlbim}R Documentation

Genome Scan for Pairs of Loci Involved in Phenotypic Trait

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,
  upper.scan = "epistasis", lower.scan = "joint", 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 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.
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.

Details

The scan and type are similar to those used in qb.scanone. However, here scan is a list and type 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 = "joint"); 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 "joint" is shorthand for the epistatics effects plus main effects, c("add", "dom"), plus any GxE terms.

The type defaults to c(upper = "LPD", lower = "LPD"). See qb.scanone for the range of possible types. Mostly the 2-D version of type provides marginal summaries for pairs of loci. However, for type "nqtl", the marginal summaries involving main effects (e.g. with scan values "joint" 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 and scan.

Author(s)

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

References

http://www.ssg.uab.edu/qtlbim

See Also

plot.qb.scanone

Examples


temp <- qb.scantwo(qbExample, chr = c(5,7,10,19))
summary(temp)
plot(temp)

[Package qtlbim version 1.6.0 Index]