as_enrichplot_object: Convert object of class 'pareg' to class 'enrichResult'.

In cbg-ethz/pareg: Pathway enrichment using a regularized regression approach

Convert object of class pareg to class enrichResult.

Description

The resulting object can be passed to any method from the enrichplot package and thus allows for nice visualizations of the enrichment results. Note: term similarities are included if available.

Usage

as_enrichplot_object(x, pvalue_threshold = 0.05)

Arguments

x	An object of class pareg.
pvalue_threshold	Treshold to select genes for count statistics.

Value

Object of class enrichResult.

Examples

df_genes <- data.frame(
  gene = paste("g", 1:20, sep = ""),
  pvalue = c(
    rbeta(10, .1, 1),
    rbeta(10, 1, 1)
  )
)
df_terms <- rbind(
  data.frame(
    term = "foo",
    gene = paste("g", 1:10, sep = "")
  ),
  data.frame(
    term = "bar",
    gene = paste("g", 11:20, sep = "")
  )
)
fit <- pareg(df_genes, df_terms, max_iterations = 10)
as_enrichplot_object(fit)

cbg-ethz/pareg documentation built on July 20, 2023, 7:30 p.m.