R: Plot the proportion of missing genotype information

plotInfo {qtl} | R Documentation

## Plot the proportion of missing genotype information

### Description

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

### Usage

    plotInfo(x, chr, method=c("entropy","variance","both"), step=1,
              off.end=0, error.prob=0.001,
              map.function=c("haldane","kosambi","c-f","morgan"),
              alternate.chrid=FALSE, fourwaycross=c("all", "AB", "CD"),
              include.genofreq=FALSE, ...)

### Arguments

`x` | An object of class `cross`. See `read.cross` for details.
`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 `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`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 `step=0`, it is are calculated only at the marker locations.
`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 (`"all"`), or just for the alleles from the first parent (`"AB"`) or from the second parent (`"CD"`).
`include.genofreq` | If TRUE, estimated genotype frequencies (from the results of `calc.genoprob` averaged across the individuals) are included as additional columns in the output.
`...` | Passed to `plot.scanone`.

### Details

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.

### Value

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.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`plot.scanone`, `plotMissing`, `calc.genoprob`, `geno.table`

### Examples

    data(hyper)

    plotInfo(hyper,chr=c(1,4))

    # save the results and view maximum missing info on each chr
    info <- plotInfo(hyper)
    summary(info)

    plotInfo(hyper, bandcol="gray70")

[Package qtl version 1.46-2 Index]