Convert enrichList to data.frame

Convert enrichList to a single data.frame, merging results

Usage

enrichList2df(
  enrichList,
  keyColname = c("ID", "Name", "pathway", "itemsetID", "Description"),
  geneColname = c("geneID", "geneNames", "Genes"),
  geneCountColname = c("gene_count", "Count", "geneCount", "geneHits"),
  pvalueColname = c("padjust", "p.adjust", "adjp", "padj", "qvalue", "qval", "q.value",
    "pvalue", "p.value", "pval", "FDR"),
  pvalueFloor = 1e-200,
  msigdbGmtT = NULL,
  geneDelim = "[,/ ]+",
  geneSep = ",",
  verbose = FALSE,
  debug = 0,
  ...
)

Arguments

enrichList

list of enrichResult or data.frame objects.

keyColname, geneColname, geneCountColname, pvalueColname

character string indicating each column to use, or a vector of column names in order of priority.

pvalueFloor

numeric lowest permitted P-value, intended to prevent using actual zero 0 which may occur sometimes when upstream processing rounds the value.

msigdbGmtT

not currently implemented.

geneDelim

character pattern used to split genes.

geneSep

character string used to join genes, default "," uses comma-delimited values.

verbose

logical indicating whether to print verbose output.

debug

integer used for debugging, with values 0, 1, 2, 3 recognized. Value 0, default, performs no debug.

...

additional arguments are ignored.

Value

data.frame with combined results across all enrichList.

Details

This function takes one or more enrichment results, and combines results into one data.frame.

• Genes are combined, reporting the unique genes in sorted order.

• numeric columns report the lowest or highest value, as appropriate:

  • P-value columns report the lowest observed value, in pvalueColname

  • Count columns report the highest observed value, except the primary count column reports the number of unique genes.

See also

Other jam conversion functions: cnet2df(), cnet2im(), enrichDF2enrichResult(), enrichList2IM()