find_overlap_gmt: Calculate overlap for species with GMT file

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Calculate overlap for species with GMT file

Description

For a species not in the iDEP database, calculate the overlap for pathway analysis.

Usage

find_overlap_gmt(
  query,
  gene_set,
  min_fdr = 0.2,
  min_size = 2,
  max_size = 10000,
  use_filtered_background,
  min_genes_background,
  max_genes_background,
  idep_data,
  processed_data
)

Arguments

query	Vector of genes to calculate the overlap on
gene_set	Gene sets from the custom GMT file to use in the overlap
min_fdr	Significant p-value to determine significantly expressed genes
min_size	Minimum size for a pathway gene set
max_size	Maximum size for a pathway gene set.

Value

A dataframe

espors/idepGolem documentation built on April 23, 2024, 1:11 p.m.