snpStats: row.summary – R documentation

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row.summary

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)

snpStats

SnpMatrix and XSnpMatrix classes and methods

v1.40.0

GPL-3

Authors

David Clayton <dc208@cam.ac.uk>

Initial release

2019-10-08