perid.summary {GenABEL} | R Documentation |
Produces call rate and heterozygosity per person
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
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"])