enrichList2df: Convert enrichList to data.frame

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

Convert enrichList to data.frame

Description

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.

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.

Value

data.frame with combined results across all enrichList.

See Also

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

jmw86069/jamenrich documentation built on Nov. 6, 2024, 7:07 p.m.