binSum: binSum

In PeakSegJoint: Joint Peak Detection in Several ChIP-Seq Samples

binSum

Description

Compute sum of compressed coverage profile in bins, using fast C code.

Usage

binSum(compressed, bin.chromStart = 0L, 
    bin.size = 1L, n.bins = 2000L, 
    empty.as.zero = FALSE)

Arguments

compressed	data.frame with integer columns chromStart, chromEnd, count.
bin.chromStart	Base before first bin.
bin.size	Bin size.
n.bins	Number of bins.
empty.as.zero	Sometimes the last few bins do not have any overlapping data in compressed. If TRUE, set these counts to 0. If FALSE, ignore these bins (returning a data.frame with fewer than n.bins rows).

Value

data.frame with n.bins rows and columns chromStart, chromEnd, count, mean.

Author(s)

Toby Dylan Hocking <[e-mail]> [aut, cre]

Examples

## bins of size 3bp.
## -1-   -3-   -5-
##    -2-   -4-
## 123456789012345 base index.
## --2---
##       --1-
##           --0-------
## Coverage profile.
profile <- data.frame(chromStart=as.integer(c(0, 6, 10)),
                      chromEnd=as.integer(c(6, 10, 10000)),
                      count=as.integer(c(2, 1, 0)))
library(PeakSegJoint)
bins <- binSum(profile,
               bin.chromStart=0L,
               bin.size=3L,
               n.bins=2000L)
library(ggplot2)
bases <- data.frame(position=1:15, base="N")
ggplot()+
  ylab("")+
  geom_text(aes(position, 0, label=base),
            data=bases)+
  geom_step(aes(chromStart+0.5, count, color=what),
            data=data.frame(profile, what="profile"),
            size=2)+
  geom_step(aes(chromStart+0.5, count, color=what),
            data=data.frame(bins, what="bin total"))+
  geom_step(aes(chromStart+0.5, mean, color=what),
            data=data.frame(bins, what="bin mean"))+
  coord_cartesian(xlim=c(0, max(bases$position)))

PeakSegJoint documentation built on April 4, 2025, 5:55 a.m.