gm_enrichreport: gm_enrichreport: GSEAmining Enrichment Report

In GSEAmining: Make Biological Sense of Gene Set Enrichment Analysis Outputs

Description

Takes the output of gm_clust, which is an hclust class object, and creates a report in pdf that contains enriched terms and enriched core genes in gene sets for each cluster. The results of each cluster are plotted in an independent page.

Usage

gm_enrichreport(
  df,
  hc,
  col_pos = "red",
  col_neg = "blue",
  top = 3,
  output = "gm_report"
)

Arguments

df	Data frame that contains at least three columns: an ID column for the gene set names, a NES column with the normalized enrichment score and a core_enrichment column containing the genes in the leading edge of each gene set separated by '/'.
hc	The output of gm_clust, which is an hclust class object.
col_pos	Color to represent positively enriched gene sets. Default is red.
col_neg	Color to represent negatively enriched gene sets. Default is blue.
top	An integer to choose the top most enriched genes to plot per cluster. The default parameter are the top 3.
output	A string to name the output pdf file.

Value

Generates a pdf file.

Examples

#' data(genesets_sel)
gs.cl <- gm_clust(genesets_sel)
## Not run: gm_enrichreport(genesets_sel, gs.cl)

GSEAmining documentation built on Nov. 8, 2020, 5:52 p.m.