pebba: PEBBA analysis

In pedrostrusso/PEBBA: PEBBA

Description

This function executes the PEBBA analysis.

Usage

pebba(file_in, gmt_file, gene_col = "Gene.symbol", logFC_col = "logFC",
  pvalue_col = "P.Value", min_genes = 100, max_genes = 1500,
  p_cut = 0.2, verbose = TRUE, analysis_name = NULL,
  results_dir = "Results", force = FALSE)

Arguments

file_in	The file or data.frame to execute the analysis on
gmt_file	The name of the gmt file containing terms and genes
gene_col	A string indicating the column with genes (Default: "Gene.symbol")
logFC_col	A string indicating the column with log fold-change values (Default: "logFC").
pvalue_col	A string indicating the column with p-values (Default: "P.Value")
min_genes	Minimum number of genes (Default: 50)
max_genes	Maximum number of genes (Default: 3000)
p_cut	P-value cutoff (Default: 0.2)
verbose	Logical. If TRUE (default), will display analysis progress messages.
analysis_name	The name to give to analysis results. (If NULL, defaults to parameter file_in without the extensions and file path; if a data.frame, defaults to 'PEBBA_analysis' when left NULL)
results_dir	The path into which results should be saved (Default: "Results").
force	Whether or not to overrwrite an existing results directory (Default: FALSE).

Value

Tables and interactive heatmaps with PEBBA results

Examples

# Run PEBBA analyses
data(example_data)
gmt_file <- system.file("extdata", "pathways.gmt", package = "PEBBA")
pebba(example_data, gmt_file)

pedrostrusso/PEBBA documentation built on May 17, 2019, 8:19 p.m.