plot.info {qtl}R Documentation

Plot the proportion of missing information in the genotype data

Description

Plot a measure of the proportion of missing information in the genotype data.

Usage

plot.info(x,chr,which=c("both","entropy","variance"),return.result=FALSE,...)

Arguments

x An object of class cross. See read.cross for details.
chr Vector specifying which chromosomes to plot.
which Indicates whether to plot the entropy version of the information, the variance version, or both.
return.result If TRUE, returns the results (as a data.frame).
... Ignored at this point.

Details

The entropy version of the missing information: for a single individual at a single genomic position, we measure the information as H = sum_g 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. This takes values between 0 and 1, assuming the value 0 when the genotypes are equally likely and 1 when one genotype has probability 0. 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 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.

Value

Calls plot.scanone to plot the proportion of missing information in the genotype data. If return.result is TRUE, the results are returned as a data.frame with class scanone.

Author(s)

Karl W Broman, kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html

See Also

plot.scanone

Examples

data(hyper)
hyper <- calc.genoprob(hyper,step=2,off.end=10)
plot.info(hyper)
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