Summarize hypergeometric enrichment results

Summarize hypergeometric enrichment results. Collapses HG result list into dataframe, and generates plots to visualize enrichments for each geneset.

summarizeHG(
  hg.res,
  fdr.filter = 1,
  fdr.threshold = 0.05,
  do.plot = T,
  show.n = 5,
  genesets = NULL,
  str.wrap.width = 25,
  col.pal = NULL,
  plt.title = "",
  pathway.name.size = 7
)

Arguments

hg.res

RunHG output list

fdr.filter

FDR filter threshold. Default 1 (i.e., include all)

fdr.threshold

FDR threshold line to draw on enrichment plots. Default is 0.05.

do.plot

Logical to generate enrichment plots for each geneset.

show.n

Number of top enrichments to visualize in plots. Ignored if do.plot == F.

genesets

Geneset list used for HG enrichment (i.e., RunHG input). Optional.

str.wrap.width

positive integer giving target line width in characters. A width less than or equal to 1 will put each word on its own line. Ignored if do.plot == F.

plt.title

Character specifying plot title. Ignored if do.plot == F.

pathway.name.size

Font size for pathway names in plots. Ignored if do.plot == F.

Value

list of summarized results

Author

Nicholas Mikolajewicz