relateChers {Ringo} | R Documentation |
This function relates found 'cher's (ChIP-enriched regions) to annotated genomic features, such as transcripts.
relateChers(pl, gff, upstream = 5000, verbose = TRUE)
pl |
Object of class cherList |
gff |
data.frame holding genomic feature annotation |
upstream |
up to how many bases upstream of annotated genomic features should chers be counted as related to that feature (see details) |
verbose |
logical; extended output to STDOUT? |
chers will be counted as related to genomic features, if
upstream
bases upstream of the feature start
One can visualize such cher-feature relations as a graph using
the Bioconductor package Rgraphviz
.
See the script 'graphChers2Transcripts.R' in Ringo's scripts
directory for an example.
An object of class cherList
with for each cher the elements
typeUpstream
and typeInside
filled in with the names
of the features that have been related to.
Joern Toedling toedling@ebi.ac.uk
# see findChersOnSmoothed for an example