ch3a: Data with a phenotype error
In qtlbook: Datasets for the R/qtl Book

Description Usage Format Details Source References See Also Examples

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

ch3a

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

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

Karl W Broman, broman@wisc.edu

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

ch3b, ch3c

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)