scanoneF: Genome scan with a single QTL model

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

Genome scan with a single QTL model

Description

Extension of the R/qtl function scanone. Genome scan with a single QTL model, with possible allowance for covariates, using several possible models for the function valued phenotype.

Usage

scanoneF(cross, pheno.cols, 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.
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 'scanone'. See 'scanone' for details.

Value

If n.perm is missing, the function returns a data.frame whose first two columns contain the chromosome IDs and cM positions. Subsequent third and fourth columns contain the SLOD and MLOD scores.

If n.perm is specified, the function returns the results of a permutation test and the output returns the matrix of two columns. The first column for SLOD and the second column for MLOD score.

Author(s)

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

See Also

scanone, scanoneM

Examples

data(exd)

# calculate QTL genotype probabilities and perform genome scan
exd <- calc.genoprob(exd, step=2)
out <- scanoneF(exd)

# summarize results
summary(out)

# Plot the results : red for slod, blue for mlod
plot(out, lod=1:2, col = c("red","blue"), ylab = "lod")


# Permutation tests
nperm <- 1000

perm1 <- scanoneF(exd, method="hk", n.perm=n.perm)
summary(perm1, alpha=c(0.05, 0.10))

# Results above the 0.05 threshold
summary(out, perms=perm1, alpha=0.05)

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