Fill holes in genotype data
Replace the genotype data for a cross with a version imputed either
by simulation with sim.geno, by the Viterbi
algorithm with argmax.geno, or simply filling in
genotypes between markers that have matching genotypes.
fill.geno(cross, method=c("imp","argmax", "no_dbl_XO", "maxmarginal"),
error.prob=0.0001,
map.function=c("haldane","kosambi","c-f","morgan"),
min.prob=0.95)cross |
An object of class |
method |
Indicates whether to impute using a single simulation
replicate from |
error.prob |
Assumed genotyping error rate used in the calculation of the penetrance Pr(observed genotype | true genotype). |
map.function |
Indicates whether to use the Haldane, Kosambi or Carter-Falconer map function when converting genetic distances into recombination fractions. |
min.prob |
For |
This function is written so that one may perform rough genome scans by marker regression without having to drop individuals with missing genotype data. We must caution the user that little trust should be placed in the results.
With method="imp", a single random imputation is performed,
using sim.geno.
With method="argmax", for each individual the most probable
sequence of genotypes, given the observed data (via
argmax.geno), is used.
With method="no_dbl_XO", non-recombinant intervals are filled
in; recombinant intervals are left missing. For example, a sequence of
genotypes like A---A---H---H---A (with A and H
corresponding to genotypes AA and AB, respectively, and with -
being a missing value) will be filled in as
AAAAA---HHHHH---A.
With method="maxmarginal", the conditional genotype
probabilities are calculated with calc.genoprob, and then at
each marker, the most probable genotype is determined. This is taken
as the imputed genotype if it has probability greater than
min.prob; otherwise it is made missing.
With method="no_dbl_XO" and method="maxmarginal",
some missing genotypes likely remain. With
method="maxmarginal", some observed genotypes may be made
missing.
The input cross object with the genotype data replaced by an
imputed version. Any intermediate calculations (such as is produced
by calc.genoprob, argmax.geno
and sim.geno) are removed.
Karl W Broman, broman@wisc.edu
data(hyper) out.mr <- scantwo(fill.geno(hyper,method="argmax"), method="mr") plot(out.mr)
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