| makeqtl {qtl} | R Documentation |
This function takes a cross object and specified chromosome numbers
and positions and pulls out the genotype probabilities or imputed
genotypes at the nearest pseudomarkers, for later use by the function
fitqtl.
makeqtl(cross, chr, pos, qtl.name, what=c("draws","prob"))
cross |
An object of class cross. See
read.cross for details. |
chr |
Vector indicating the chromosome for each QTL. (These should be character strings referring to the chromosomes by name.) |
pos |
Vector (of same length as chr) indicating the
positions on the chromosome to be taken. If there is no marker or
pseudomarker at a position, the nearest position is used. |
qtl.name |
Optional user-specified name for each QTL, used in the
drop-one-term ANOVA table in fitqtl.
If unspecified, the names will be of the form "Chr1@10" for a
QTL on Chromsome 1 at 10 cM. |
what |
Indicates whether to pull out the imputed genotypes or the genotype probabilities. |
This function will take out the genotype probabilities and imputed
genotypes if they are present in the input cross object. If both
fields are missing in the input object, the function will report an
error. Before running this function, the user must have first run either
sim.geno (for what="draws") or
calc.genoprob (for what="prob").
An object of class qtl with the following elements (though only
one of geno and prob will be included, according to
whether what is given as "draws" or "prob"):
|
Imputed genotypes. |
|
Genotype probabilities. |
|
User-defined name for each QTL, or a name of the
form "Chr1@10". |
|
QTL names of the form "Q1", "Q2",
etc. |
|
Input vector of chromosome numbers. |
|
Input vector of chromosome positions. |
|
Number of QTLs. |
|
Number of individuals. |
|
A vector indicating the number of genotypes for each QTL. |
Hao Wu; Karl W Broman, kbroman@biostat.wisc.edu
fitqtl, calc.genoprob,
sim.geno, dropfromqtl,
replaceqtl, addtoqtl, summary.qtl,
reorderqtl
data(fake.f2)
# take out several QTLs and make QTL object
qc <- c("1", "6", "13")
qp <- c(25.8, 33.6, 18.63)
fake.f2 <- subset(fake.f2, chr=qc)
fake.f2 <- sim.geno(fake.f2, n.draws=8, step=2, err=0.001)
qtl <- makeqtl(fake.f2, qc, qp, what="draws")
summary(qtl)