relatePeaks {Ringo} | R Documentation |
This function relates found peaks to annotated genomic features, such as transcripts.
relatePeaks(pl, gff, upstream = 5000, verbose = TRUE)
pl |
Object of class peakList |
gff |
data.frame holding genomic feature annotation |
upstream |
up to how many bases upstream of annotated genomic features should peaks be counted as related to that feature (see details) |
verbose |
logical; extended output to STDOUT? |
Peaks will be counted as related to genomic features, if
upstream
bases upstream of the feature start
One can visualize such peak-feature relations as a graph using
the Bioconductor package Rgraphviz
.
See the script 'graphPeaks2Transcripts.R' in Ringo's scripts
directory for an example.
An object of class peakList
with for each peak the elements
typeUpstream
and typeDownstream
filled in with the names
of the features that have been related to.
Joern Toedling toedling@ebi.ac.uk
# see findPeaksOnSmoothed for an example