cand.reg {qtlyeast} | R Documentation |
Find candidate regulators based on QTL mapping. Identify cis-acting. Find co-mapping targets.
data(ko.list) data(cand.reg) data(cis.cand.reg) data(comap.targets)
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
The ko.list
comes from that TransFac yeast database (when? version?).
Brem Kruglyak (2005) Science
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))