PeakSegJointFaster {PeakSegJoint} | R Documentation |
PeakSegJointFaster
Description
Run the PeakSegJointFaster heuristic optimization algorithm, for several bin.factor parameter values, keeping only the most likely model found. This gives an approximate solution to a multi-sample Poisson maximum likelihood segmentation problem. Given S samples, this function computes a sequence of S+1 PeakSegJoint models, with 0, ..., S samples with an overlapping peak (maximum of one peak per sample). It also computes for G groups, the seq of G+1 models, with 0, ..., G groups with an overlapping peak.
Usage
PeakSegJointFaster(profiles,
bin.factor.vec = 2:7)
Arguments
profiles |
data.frame with columns sample.id, sample.group, chromStart, chromEnd, count. |
bin.factor.vec |
Size of bin pyramid. Bigger values result in slower computation. |
Value
List of model fit results.
Author(s)
Toby Dylan Hocking
Examples
library(PeakSegJoint)
data(H3K36me3.TDH.other.chunk1, envir=environment())
some.counts <- subset(
H3K36me3.TDH.other.chunk1$counts,
43000000 < chromEnd &
chromStart < 43200000)
some.counts$sample.group <- some.counts$cell.type
fit <- PeakSegJointFaster(some.counts, 2:7)
if(interactive() && require(ggplot2)){
both <- with(fit, rbind(
data.frame(model="sample", sample.modelSelection),
data.frame(model="group", group.modelSelection)))
ggplot()+
ggtitle("model selection functions")+
scale_size_manual(values=c(sample=2, group=1))+
geom_segment(aes(min.log.lambda, complexity,
color=model, size=model,
xend=max.log.lambda, yend=complexity),
data=both)+
xlab("log(penalty)")+
ylab("model complexity (samples or groups with a common peak)")
}
[Package PeakSegJoint version 2024.6.27 Index]