PeakSegDP {PeakSegDP} | R Documentation |
Compute the PeakSeg model on a data.frame of compressed sequence reads.
PeakSegDP(compressed, maxPeaks)
compressed |
data.frame with columns chromStart, chromEnd, count. |
maxPeaks |
maximum number of peaks to consider. |
Toby Dylan Hocking, Guillem Rigaill
library(PeakSegDP) data(chr11ChIPseq, envir=environment()) one <- subset(chr11ChIPseq$coverage, sample.id=="McGill0002")[10000:12000,] fit <- PeakSegDP(one, 3L) if(interactive() && require(ggplot2)){ ggplot()+ geom_step(aes(chromStart/1e3, count), data=one)+ geom_segment(aes(chromStart/1e3, mean, xend=chromEnd/1e3, yend=mean), data=fit$segments, color="green")+ geom_segment(aes(chromStart/1e3, 0, xend=chromEnd/1e3, yend=0), data=subset(fit$segments, status=="peak"), size=3, color="deepskyblue")+ theme_bw()+ theme(panel.margin=grid::unit(0, "cm"))+ facet_grid(peaks ~ ., scales="free", labeller=function(df){ s <- ifelse(df$peaks==1, "", "s") df$peaks <- paste0(df$peaks, " peak", s) df }) }