scglue.genomics.window_graph
- scglue.genomics.window_graph(left, right, window_size, left_sorted=False, right_sorted=False, attr_fn=None)[source]
Construct a window graph between two sets of genomic features, where features pairs within a window size are connected.
- Parameters
left (
typing.Union
[scglue.genomics.Bed
,str
]) – First feature set, either aBed
object or path to a bed fileright (
typing.Union
[scglue.genomics.Bed
,str
]) – Second feature set, either aBed
object or path to a bed filewindow_size (
int
) – Window size (in bp)left_sorted (
bool
) – Whetherleft
is already sortedright_sorted (
bool
) – Whetherright
is already sortedattr_fn (
typing.Optional
[typing.Callable
[[pybedtools.cbedtools.Interval
,pybedtools.cbedtools.Interval
,float
],typing.Mapping
[str
,typing.Any
]]]) –Function to compute edge attributes for connected features, should accept the following three positional arguments:
l: left interval
r: right interval
d: signed distance between the intervals
By default no edge attribute is created.
- Return type
- Returns
graph – Window graph