Author
Joe DeRose and Rick Mortensen
Rick Mortensen
Methods
Method new()
Builds junction class, grl must be GRangesList with each GRanges of length 2 JUNCTION
Empty junctions are removed
If grl is empty GRangesList, Junctions class is empty
Arguments
grl
GRangesList of signed breakpoint pairs
Method removeDups()
Removes duplicate junctions in this Junction Object
this Junction Object has no duplicate junctions
Method gw()
Returns a gWalk representing the left -> right traversal of this junction +- padding
Returns
GRangesList of the junctions in this Junction Object
Allows subseting of the Junction object using bracket notation
Arguments
i
integer or self$length logical vector specifying subset
Method set()
set metadata for junction object
Details
sets metadata to either a scalar or vector
where the vector is the same length as the junction object
```
jj$set(cn = 7)
jj$set(cn = c(1,2,3))
jj$set(col = c("red", "blue", "green"))
```
(after setting, metadata is accessible through $dt accessor)
Prints out the Junction Object. Prints the length and the GRangesList of the junctions.
Method clone()
The objects of this class are cloneable with this method.
Arguments
deep
Whether to make a deep clone.