as.data.frame for an object of class pareg. — as.data.frame.pareg • pareg

Retrieve dataframe with enrichment information.

# S3 method for pareg
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

x: An object of class pareg.
row.names: Optional character vector of rownames.
optional: Allow optional arguments.
...: Additional arguments.

Value

Dataframe containing enrichment score and name for each pathway.

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)
#> Loaded Tensorflow version 2.3.0
as.data.frame(fit)
#>   term enrichment
#> 1  bar -0.7535364
#> 2  foo -0.5733565