yeast.orf {qtlyeast} | R Documentation |
The Brem and Kruglyak (2005) Science yeast data organized into an R/qtl cross object.
data(yeast.orf) data(yeast.annot) data(highlod.orf) data(highlodmax.orf) data(perm.orf)
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.
Brem and Kruglyak (2001) Science.
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