R: Create table of genotype distributions

geno.table {qtl} | R Documentation

## Create table of genotype distributions

### Description

Create table showing the observed numbers of individuals with each genotype at each marker, including P-values from chi-square tests for Mendelian segregation.

### Usage

    geno.table(cross, chr, scanone.output=FALSE)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`chr` | Optional vector indicating the chromosomes to consider. 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.
`scanone.output` | If TRUE, give result in the form output by `scanone`, so that one may use `plot.scanone`, etc.

### Details

The P-values are obtained from chi-square tests of Mendelian segregation. In the case of the X chromosome, the sexes and cross directions are tested separately, and the chi-square statistics combined, and so the test is of whether any of the groups show deviation from Mendel's rules.

### Value

If `scanone.output=FALSE`, the output is a matrix containing, for each marker, the number of individuals with each possible genotype, as well as the number that were not typed. The first column gives the chromosome ID, and the last column gives P-values from chi-square tests of Mendelian segregation.

If `scanone.output=TRUE`, the output is of the form produced by `scanone`, with the first two columns being chromosome IDs and cM positions of the markers. The third column is -log10P from chi-square tests of Mendelian segregation. The fourth column is the proportion of missing data. The remaining columns are the proportions of the different genotypes (among typed individuals).

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`summary.cross`, `drop.markers`, `drop.nullmarkers`

### Examples

    data(listeria)
    geno.table(listeria)

    geno.table(listeria, chr=13)

    gt <- geno.table(listeria)
    gt[gt$P.value < 0.01,]

    out <- geno.table(listeria, scanone.output=TRUE)
    plot(out)
    plot(out, lod=2)

[Package qtl version 1.46-2 Index]