ch3a: Data with a phenotype error

In qtlbook: Datasets for the R/qtl Book

Data with a phenotype error

Description

Anonymous data with a phenotype error and a pair of individuals with very similar phenotypes.

Usage

ch3a

Format

An object of class cross. See qtl::read.cross() for details.

Details

A backcross with 234 individuals, each with five phenotypes and typed at 166 markers.

Source

Karl W Broman, [e-mail]

References

Broman, K. W. and Sen, S. (2009) A Guide to QTL Mapping with R/qtl. Springer, New York.

See Also

ch3b, ch3c

Examples

data(ch3a)

# phenotype problem
pairs(ch3a$pheno)
ch3a$pheno[ch3a$pheno[,4]==0,] # individual 159

# individuals with similar genotypes
library(qtl)
cg <- comparegeno(ch3a)
hist(cg, breaks=200)
max(cg[cg < 1])
which(cg == max(cg[cg < 1]), arr.ind=TRUE)

qtlbook documentation built on June 8, 2025, 11:20 a.m.