summary.mGST {massiveGST}

Generate summary tables

Description

This method handles the result of massiveGST function, to provide views of the table.

Usage

## S3 method for class 'mGST'
summary(object, 
  cols_to_remove = "link", 
  order_by = c("relevance", "NES", "logit2NES", "p.value", "BH.value", "bonferroni"), 
  top = NULL, 
  as.formattable = FALSE, 
  ...
)

Arguments

object

a data structure coming from the massiveGST function

cols_to_remove

A character list of the columns to remove from the output.

order_by

a character string specifying which marginal ordering has to be applied to the output; must be one of "relevance" (default), "NES", "logit2NES", "p.value", "BH.value", and "bonferroni"

top

an integer to trim the table to the first 'top' rows.

as.formattable

a logical value (default = FALSE) to provide a formatted output with the help of formattable package.

...

Arguments to be passed to methods

Value

A data frame.

Author(s)

Stefano M. Pagnotta

See Also

massiveGST

Examples

library(massiveGST)

# get the gene profile
fname <- system.file("extdata", package="massiveGST")
fname <- file.path(fname, "pre_ranked_list.txt")
geneProfile <- get_geneProfile(fname)

# get the gene-sets
geneSets <- get_geneSets_from_msigdbr(category = "H", what = "gene_symbol")

# run the function
ans <- massiveGST(geneProfile, geneSets, alternative = "two.sided")

summary(ans)
summary(ans, as.formattable = TRUE, order_by = "NES", top = 10)