scanoneM: QTL scan using dimensional reduction.

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

QTL scan using dimensional reduction.

Description

Genome scan with a single QTL model using dimensional reduction

Usage

scanoneM(
  cross,
  Y,
  tol = 0.0000001,
  n.perm = 0,
  method = c("hk", "f", "sl", "ml"),
  pheno.cols
)

Arguments

cross	An object of class "cross". See read.cross for details.
Y	Dimension-reduced data set.
tol	Tolerance; passed to lm.fit
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.
method	The "hk" option use multi-trait QTL mapping proposed by Haley and Knott. The "f" option use an FLOD score.
pheno.cols	Columns in the phenotype matrix to be used as the phenotype.

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, scanoneF

Examples

data(simspal)


# Genotype probabilities for H-K
simspal <- calc.genoprob(simspal)

# dimensional reduction of Y
cvout <- cvfold(simspal, basisset = 5:50, fold = 20)
plot(cvout) ## take nbasis = 15
Y <- calcfunpca(simspal, criteria=.999, nbasis = 15)$Y

# do multitrait mapping
out.hk <- scanoneM(simspal, Y=Y, method="hk")
out.f  <- scanoneM(simspal, Y=Y, method="f")
out.sl <- scanoneM(simspal, Y=Y, method="sl")
out.ml <- scanoneM(simspal, Y=Y, method="ml")

# Summarize results
summary(out.hk)
summary(out.f)
summary(out.sl)
summary(out.ml)

# Plot the results
par(mfrow=c(3,1))
plot(out.hk)
plot(out.f)
plot(out.sl, out.ml)

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