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)