Description Usage Arguments Details Value Author(s) See Also Examples
Plot a measure of the proportion of missing information in the genotype data.
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x |
An object of class |
chr |
Optional vector indicating the chromosomes to plot.
This should be a vector of character strings referring to chromosomes
by name; numeric values are converted to strings. Refer to
chromosomes with a preceding |
method |
Indicates whether to plot the entropy version of the information, the variance version, or both. |
step |
Maximum distance (in cM) between positions at which the
missing information is calculated, though for |
off.end |
Distance (in cM) past the terminal markers on each chromosome to which the genotype probability calculations will be carried. |
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. |
alternate.chrid |
If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished. |
fourwaycross |
For a phase-known four-way cross, measure missing
genotype information overall ( |
include.genofreq |
If TRUE, estimated genotype frequencies (from
the results of
|
... |
Passed to |
The entropy version of the missing information: for a single individual at a single genomic position, we measure the missing information as H = sum p[g] log p[g] / log n, where p[g] is the probability of the genotype g, and n is the number of possible genotypes, defining 0 log 0 = 0. This takes values between 0 and 1, assuming the value 1 when the genotypes (given the marker data) are equally likely and 0 when the genotypes are completely determined. We calculate the missing information at a particular position as the average of H across individuals. For an intercross, we don't scale by \log n but by the entropy in the case of genotype probabilities (1/4, 1/2, 1/4).
The variance version of the missing information: we calculate the average, across individuals, of the variance of the genotype distribution (conditional on the observed marker data) at a particular locus, and scale by the maximum such variance.
Calculations are done in C (for the sake of speed in the presence of
little thought about programming efficiency) and the plot is created
by a call to plot.scanone
.
Note that summary.scanone
may be used to display
the maximum missing information on each chromosome.
An object with class scanone
: a data.frame with columns the
chromosome IDs and cM positions followed by the entropy and/or
variance version of the missing information.
Karl W Broman, kbroman@biostat.wisc.edu
plot.scanone
,
plotMissing
, calc.genoprob
,
geno.table
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