annotateRegions {derfinder} | R Documentation |
This function takes the regions found in calculatePvalues and assigns them genomic states contructed with makeGenomicState. The main workhorse functions are countOverlaps and findOverlaps.
annotateRegions(regions, genomicState, annotate = TRUE, ...)
regions |
The |
genomicState |
A GRanges object created with makeGenomicState.
It can be either the |
annotate |
If |
... |
Arguments passed to other methods and/or advanced arguments. Advanced arguments:
Passed to extendedMapSeqlevels, countOverlaps and findOverlaps-methods. |
You might want to specify arguments such as minoverlap
to control
how the overlaps are determined. See findOverlaps
for further details.
A list with elements countTable
and annotationList
(only if annotate=TRUE
).
This is a data.frame with the number of overlaps from the
regions vs the genomic states with one type per column. For example, if
fullOrCoding='full'
then the columns are exon
,
intergenic
and intron
.
This is a GRangesList
with the genomic states
that overlapped with the regions. The
names of this GRangesList
correspond to the region index in
regions
.
Andrew Jaffe, Leonardo Collado-Torres
makeGenomicState, calculatePvalues
## Annotate regions, first two only annotatedRegions <- annotateRegions(regions=genomeRegions$regions[1:2], genomicState=genomicState$fullGenome, minoverlap=1) annotatedRegions