Convert enrichList to IM incidence matrix
Arguments
- enrichList
list
ofenrichResult
objects- addAnnotations
logical
not implemented, this argument is paired withGmtT
.- keyColname
character
used to match colnames, referring to the unique identifier. Values in this column will become the column headers in the resulting incidence matrix.- valueColname
character
used to match colnames to determine the value to place in each cell of the incidence matrix.- emptyValue
numeric
value used to fill empty cells in the incidence matrix. WhenNULL
andvalueColname
contains "gene", "count", "num", "hit" thenemptyValue=0
, otherwiseemptyValue=1
is used with the assumption thatvalueColname
refers to P-values.- verbose
logical
indicating whether to print verbose output.- GmtT
(not currently implemented), alternative gene set object format that uses
arules::transactions
class, an efficient object with robust access functions inarules
.- ...
additional arguments are ignored.
Details
This function takes a list
of enrichResult
objects
and creates an incidence matrix using the value defined
by valueColname
.
TODO: Port to use venndir::list2im_value()
, which itself
may be moved to its own proper R package for set and list
manipulation, without the dependencies incurred by venndir
.
See also
Other jam conversion functions:
cnet2df()
,
cnet2im()
,
enrichDF2enrichResult()
,
enrichList2df()
,
enrichMapJam()