plotProfiles: Plotting ChIP profiles of one or more clusters

In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description

plotProfiles plots the ChIP profiles of one or more clusters. Additionally on can display the distribution of e.g. gene expression in the clusters.

Usage

plotProfiles(profiles, mfcol=NULL, mfrow=NULL, ylab="intensity", xlab="position", histograms=NULL, cluster, profileplot=T, meanprofile=T, ...)

Arguments

profiles	a list constructed by the function getProfiles().
mfcol	see ?par
mfrow	see ?par
ylab	see ?par
xlab	see ?par
histograms	a list of named vectors. Density plots are created for every vector and cluster.
cluster	A named integer vector, that maps the features to the cluster.
profileplot	should a clusterplot be shown?
meanprofile	should the mean profiles of each cluster be plotted??
...	arguments, passed to plot.default

Author(s)

Benedikt Zacher [e-mail]

See Also

density, profileplot

Examples

## 
sampls = 100
probes = 63
clus = matrix(rnorm(probes*sampls,sd=1),ncol=probes)
clus= rbind( t(t(clus)+sin(1:probes/10))+1:nrow(clus)/sampls , t(t(clus)+sin(pi/2+1:probes/10))+1:nrow(clus)/sampls )
clustering = kmeans(clus,3)$cluster
names(clustering) <- 1:length(clustering)


profiles <- apply(clus, 1, function(x) {list(upstream=x[1:20], region=x[21:43], downstream=x[44:63])})
names(profiles) <- 1:length(clustering)
profiles <- list(profile=profiles, upstream=20, downstream=20, borderNames=c("start", "stop"))

plotProfiles(profiles, cluster=clustering, ylim=c(-1,2.5), type="l", lwd=2)

Starr documentation built on April 28, 2020, 7:52 p.m.