plot.info {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

plot.info(x, chr, method=c("both","entropy","variance"), ...)

### Arguments

`x` |
An object of class `cross` . See
`read.cross` for details. |

`chr` |
Vector specifying the chromosomes to plot. |

`method` |
Indicates whether to plot the entropy version of the
information, the variance version, or both. |

`...` |
Passed to `plot.scanone` . |

### Details

The missing information is calculated using the multipoint genotype
probabilities calculated with `calc.genoprob`

.

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, kbroman@jhsph.edu

### See Also

`plot.scanone`

,
`plot.missing`

### Examples

data(hyper)
hyper <- calc.genoprob(hyper, step=2.5, off.end=5)
plot.info(hyper,chr=c(1,4))
# save the results and view maximum missing info on each chr
info <- plot.info(hyper)
summary(info)

[Package

*qtl* version 0.98-57

Index]