| qb.scantwo {qtlbim} | R Documentation |
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.
qb.scantwo(qbObject, epistasis = TRUE, scan, type.scan, upper.scan = "epistasis", lower.scan = "full", covar, adjust.covar, chr, min.iter = 1, verbose = FALSE, ...)
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. |
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.
Returns an object of class qb.scantwo (a data frame) containing
effects selected according to type.scan and scan.
Brian S. Yandell, yandell@stat.wisc.edu
data(qbExample) temp <- qb.scantwo(qbExample) summary(temp) plot(temp)