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]