scantwoF: Two-dimensional genome scan with a two-QTL model for function...

In ikwak2/funqtl: QTL Mapping for Function-Valued Traits

Two-dimensional genome scan with a two-QTL model for function valued trait data.

Description

Extension of the R/qtl function scantwo. Two-dimensional genome scan with a two-QTL model for function valuded trait data.

Usage

scantwoF(cross, pheno.cols, usec = c("slod", "mlod"), n.perm, ...)

Arguments

cross	An object of class "cross". See read.cross for details.
pheno.cols	Columns in the phenotype matrix to be used as the phenotype.
usec	Which method to use ("slod" or "mlod") in the two-QTL scan.
n.perm	If specified, a permutation test is performed rather than an analysis of the observed data. This argument defines the number of permutation replicates.
...	More parameters controled in 'scantwo'. See 'scantwo' for details.

Value

If n.perm is missing, the function returns a list with class "scantwo" and containing three components. The first component is a matrix of dimension [tot.pos x tot.pos]; the upper triangle contains the (S/MLOD) scores for the additive model, and the lower triangle contains the LOD scores for the full model. The diagonal contains the results of a single-QTL scan. The second component of the output is a data.frame indicating the locations at which the two-QTL (S/MLOD) scores were calculated. The first column is the chromosome identifier, the second column is the position in cM, the third column is a 1/0 indicator for ease in later pulling out only the equally spaced positions, and the fourth column indicates whether the position is on the X chromosome or not. The final component is a version of the results of 'scanone' including sex and/or cross direction as additive covariates, which is needed for a proper calculation of conditional (S/MLOD) scores.

If n.perm is specified, the function returns a list with six different LOD scores from each of the permutation replicates. ... need more ..

Author(s)

Il-Youp Kwak, <email: [e-mail]>

See Also

scantwo, codescanoneF

Examples

data(exd)
exd <- calc.genoprob(exd, step = 0)
out <-scantwoF(exd, method = "hk", usec="slod")
plot(out)

# Permutation tests
n.perm <- 1000
## Not run: permo <- scantwoF(exd, method="hk", n.perm=n.perm)
summary(permo, alpha=0.05)
## End(Not run)

ikwak2/funqtl documentation built on April 20, 2022, 3:58 a.m.