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Convert enrichList to IM incidence matrix

Source: R/jamenrich-base.r
enrichList2IM.Rd

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, default NA.

  • NA is used by default, indicating absence of a value.

  • 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. In future it may enable passing additional annotations associated with each gene set, including description, source, category, etc.

...

additional arguments are ignored.

Value

incidence matrix with numeric values using the the enrichment P-value (or FDR or Q-value as defined). Technically it is a "value incidence matrix" where non-NA values are derived from the source data, and NA represents absense of a value in the source data. It is possible to have a value '0' (pure zero) which represents presence of a value, where that value was '0', if the P-value reported by an enrichment tool rounded to zero.

Details

This function takes a list of enrichResult objects and creates an incidence matrix using the value defined by valueColname.

TODO: Consider using 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()