PeakSegDP: PeakSegDP In PeakSegDP: Dynamic Programming Algorithm for Peak Detection in ChIP-Seq Data

Description

Compute the PeakSeg model on a data.frame of compressed sequence reads.

Usage

 `1` ```PeakSegDP(compressed, maxPeaks) ```

Arguments

 `compressed` data.frame with columns chromStart, chromEnd, count. `maxPeaks` maximum number of peaks to consider.

Author(s)

Toby Dylan Hocking, Guillem Rigaill

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25``` ```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 }) } ```

PeakSegDP documentation built on Aug. 16, 2017, 1:02 a.m.