cand.reg {qtlyeast}R Documentation

Candidate regulators for yeast.

Description

Find candidate regulators based on QTL mapping. Identify cis-acting. Find co-mapping targets.

Usage

data(ko.list)
data(cand.reg)
data(cis.cand.reg)
data(comap.targets)

Format

A data frame with 135 observations on the following 6 variables.

gene

a character vector

phys.chr

a character vector

phys.pos

a numeric vector

peak.chr

a numeric vector

peak.pos

a numeric vector

peak.lod

a numeric vector

Details

The ko.list comes from that TransFac yeast database (when? version?).

References

Brem Kruglyak (2005) Science

See Also

yeast.orf

Examples

library(qtlhot)
data(highlod.orf)
data(yeast.annot)
data(ko.list)
cand.reg <- GetCandReg(highlod.orf, yeast.annot, names(ko.list))
dim(cand.reg)
head(cand.reg)
##
cis.cand.reg <- GetCisCandReg(highlod.orf, cand.reg)
dim(cis.cand.reg)
head(cis.cand.reg)
##
comap.targets <- GetCoMappingTraits(highlod.orf, cand.reg)
summary(sapply(comap.targets, length))
comap.targets[[7]]
length(unlist(comap.targets))

[Package qtlyeast version 1.0.4 Index]