enrichList2IM: Convert enrichList to IM incidence matrix

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Convert enrichList to IM incidence matrix

Description

Convert enrichList to IM incidence matrix

Usage

enrichList2IM(
  enrichList,
  addAnnotations = TRUE,
  keyColname = c("ID", "Name", "pathway", "itemsetID"),
  valueColname = c("qvalue", "q.value", "padj", "pvalue", "p.value"),
  emptyValue = NA,
  verbose = FALSE,
  GmtT = NULL,
  ...
)

Arguments

enrichList	list of enrichResult objects
addAnnotations	logical not implemented, this argument is paired with GmtT.
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. When NULL and valueColname contains "gene", "count", "num", "hit" then emptyValue=0, otherwise emptyValue=1 is used with the assumption that valueColname 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 in arules.
...	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()

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.