row.summary {snpStats} | 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 `"SnpMatrix"` or `"XSnpMatrix"`

### Usage

    row.summary(object)
    col.summary(object, rules = NULL, uncertain = TRUE)

### Arguments

`object` | genotype data as a `SnpMatrix-class` or `XSnpMatrix-class` object
`rules` | An object of class `"ImputationRules"`. If supplied, the rules coded in this object are used, together with the snp genotype data in `object`, to generate imputed SNPs. The column summary of these imputed data are then returned
`uncertain` | If `TRUE` uncertain genotypes are used in calculation of allele and genotype frequencies (by scoring as posterior expectations). Otherwise, and for Hardy-Weinberg tests, they are ignored

### 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 Certain.calls: Proportion of called SNPs with certain calls Heterozygosity: Proportion of called SNPs which are heterozygous Uncertain calls are ignored for calculating the heterozygosity.
`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 Certain.calls: Proportion of called SNPs with certain calls RAF: The "risk" allele (allele `B`) frequency 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 `"XSnpMatrix"`, 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 dc208@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 snpStats version 1.40.0 Index]