row.summary {snpMatrix} | R Documentation

## Summarize rows or columns of a snp matrix

### Description

These function calculates summary statistics of each row or column of call rates and heterozygosity for each row of a an object of class `"snp.matrix"` or `"X.snp.matrix"`

### Usage

    row.summary(object)
    col.summary(object)

### Arguments

`object` | genotype data as a `snp.matrix-class` or `X.snp.matrix-class` object

### Value

`row.summary` | returns a data frame with rows corresponding to rows of the input object and with columns/elements: Call.rate Proportion of SNPs called Heterozygosity Proportion of called SNPs which are heterozygous
`col.summary` | returns a data frame with rows corresponding to columns of the input object and with columns/elements: Calls The number of valid calls Call rate The proportion of genotypes called MAF The minor allele frequency P.AA The frequency of homozygous genotype 1 (A/A) P.AB The frequency of heterozygous genotype 2 (A/B) P.BB The frequency of homozygous genotype 3 (B/B) z.HWE A z-test for Hardy-Weinberg equilibrium For objects of class `"X.snp.matrix"`, the following additional columns are returned: P.AY The frequency of allele A in males P.BY The frequency of allele B in males Calls.female The number of valid calls in females (only these calls are used in the z-test for HWE)

### Note

The current version of `row.summary` does not deal with the X chromosome differently, so that males are counted as homozygous.

### Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

### Examples

    data(testdata)
    rs <- row.summary(Autosomes)
    summary(rs)
    cs <- col.summary(Autosomes)
    summary(cs)
    cs <- col.summary(Xchromosome)
    summary(cs)

[Package snpMatrix version 1.8.0 Index]