yeast.orf {qtlyeast}R Documentation

Cross object with edited yeast data from Brem and Kruglyak

Description

The Brem and Kruglyak (2005) Science yeast data organized into an R/qtl cross object.

Usage

data(yeast.orf)
data(yeast.annot)
data(highlod.orf)
data(highlodmax.orf)
data(perm.orf)

Details

yeast.orf is a cross object (see read.cross) containing Brem and Kruglyak (2001) yeast data with 112 individuals, 2956 markers, and 5740 phenotypes. Data were cleaned and updated by Jun Zhu and others at Sage Bionetworks before being organized by Elias Chaibub Neto and Brian Yandell into this package.

References

Brem and Kruglyak (2001) Science.

See Also

cand.reg, highlod

Examples

library(qtlhot)
data(yeast.orf)
summary(yeast.orf)
## Not run: 
yeast.orf <- calc.genoprob(yeast.orf, step = 2)
scan.orf <- scanone(yeast.orf, pheno.col = seq(nphe(yeast.orf)), method = "hk")
save(scan.orf, file = "scan.orf.RData", compress = TRUE)
highlod.orf <- highlod(scan.orf, lod.thr = 3.47, drop.lod = 1.5)

## End(Not run)
data(highlod.orf)
summary(highlod.orf, threshold = 80)
plot(highlod.orf)
abline(h = 80, lwd = 2, col = "red", lty = 2)
##
## Not run: 
set.seed(12345)
perm.orf <- scanone(cross, method = "hk", n.perm = 1000)

## End(Not run)
summary(perm.orf)
lod.thr <- c(summary(perm.orf, alpha = 0.05))
lod.thr

[Package qtlyeast version 1.0.4 Index]