makeBioRegionFromGranges | R Documentation |
make windows from granges object
makeBioRegionFromGranges(gr, by, type, upstream = 1000, downstream = 1000)
gr |
a grange object contain region of interest |
by |
specify be users, e.g. gene, insulator, enhancer |
type |
one of "start_site", "end_site", "body" |
upstream |
upstream from start site or end site, can be NULL if the type == 'body' |
downstream |
downstream from start site or end site, can be NULL if the type == 'body' |
makeBioRegionFromGranges()
function can make bioregion from granges object.
The differences between makeBioRegionFromGranges()
and getBioRegion()
is that
getBioRegion()
get the region object from txdb
object but
makeBioRegionFromGranges()
get the region from the granges object provided by users.
For example, txdb
object do not contain insulator or enhancer regions. Users can
provide these regions through self-made granges object
There are three kinds of regions, start_site
, end_site
and body
.
We take enhancer region to explain the differences of these three regions. enhancer: chr1 1000 1400.
body
region refers to the 1000-1400bp.
start_site
region with upstream = 100, downstream = 100
refers to 900-1100bp.
end_site
region with upstream = 100, downstream = 100
refers to 1300-1500bp.
In makeBioRegionFromGranges()
, upstream
and downstream
can be
NULL
if the type == 'body'
. by
should be specified by users and
can not be omitted. by
parameter will be used to made labels. type
should also
be specified.
https://github.com/YuLab-SMU/ChIPseeker/issues/189
GRanges object
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