perid.summary: Summary of marker data per person
In GenABEL: genome-wide SNP association analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Produces call rate and heterozygosity per person

1	perid.summary(data, snpsubset, idsubset, ... )

`data`	object of `snp.data-class`
`snpsubset`	Index, character or logical vector with subset of SNPs to run analysis on. If missing, all SNPs from `data` are used for analysis.
`idsubset`	Index, character or logical vector with subset of IDs to run analysis on. If missing, all people from `data` are used for analysis.
`...`	additional parameters to be passed to `hom`

This function facilitates quality control of genomic data. E.g. extreme outliers for heterozygosity indicate possibly contaminated DNA samples, while low call rate of a person may indicate poor DNA quality.

A matrix, giving per person (row) its' average heterozygosity ("Het" column) and call rate ("CallPP"), over all SNPs

Yurii Aulchenko

check.marker, summary.snp.data, snp.data-class

require(GenABEL.data)
data(ge03d2c)
a <- perid.summary(data=ge03d2c,snps=c(1:100),ids=c(1:10))
a
a <- perid.summary(data=ge03d2c)
hist(a[,"CallPP"])
hist(a[,"Het"])