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Perform enrichment analysis

Source: R/enrichit.R
EnrichIt.Rd

Perform enrichment analysis

Usage

EnrichIt(
  userlist,
  dbs,
  method = ifelse(tolower(style[1]) == "enrichr", "fisher", "hypergeometric"),
  use_matched_only = ifelse(tolower(style[1]) == "enrichr", FALSE, TRUE),
  padjust_method = c("BH", "bonferroni", "holm", "hochberg", "hommel", "BY", "fdr"),
  background = NULL,
  style = c("enrichr", "Enrichr", "clusterProfiler", "ClusterProfiler",
    "clusterprofiler"),
  return_all = FALSE
)

Arguments

userlist

Vector of user-provided genes

dbs

List of gene sets or paths to GMT files It can be a vector of database names. You can set the names of the vector, which will be used as the database names. Otherwise a list is expected, where each element is a database (e.g. parsed from a gmt file). If a database is given directly (without a name), the expression of this argument will be used as the database name.

method

Method for computing p-value, either "fisher" or "hypergeometric" When style is "enrichr", the method defaults to "fisher". When style is "clusterProfiler", the method defaults to "hypergeometric".

use_matched_only

Logical, whether to use only matched genes against the gene sets. This will affect the number of genes in the user list when computing the p-value. By default, when style is "enrichr", this is set to FALSE. When style is "clusterProfiler", this is set to TRUE.

padjust_method

Method for adjusting p-values, either "BH", "bonferroni", "holm", "hochberg", "hommel", "BY", "fdr"

background

Vector of all genes in the universe or a number of genes in the universe. If NULL, the number of genes in the gene set will be used. For "enrichr", the default is 20,000. For "clusterProfiler", the default is the number of unique genes in the gene set. Note that for "enrichr", if a vector is given, the length of it will be used, no checking will be done to see if userlist and genes from dbs are in the vector.

style

Style of the output, either "enrichr" or "clusterProfiler"

return_all

Logical, whether to return all results (all gene sets in dbs) or only those with at least one gene in the user list.

Value

A data frame with the results. When style is "enrichr", the columns are:

  • Database: Name of the database

  • Term: Name of the term

  • Overlap: Number of genes in the user list and the gene set

  • P.value: p-value from the enrichment test

  • Adjusted.P.value: Adjusted p-value from the enrichment test

  • Odds.Ratio: Odds ratio from the enrichment test

  • Combined.Score: Combined score from the enrichment test

  • Genes: Genes in the user list that are also in the gene set

  • Rank: Rank of the term based on the combined score

When style is "clusterProfiler", the columns are:

  • ID: Name of the term

  • Description: Description of the term

  • GeneRatio: Ratio of genes in the user list and the gene set

  • BgRatio: Ratio of genes in the gene set and the universe

  • Count: Number of genes in the user list that are also in the gene set

  • pvalue: p-value from the enrichment test

  • p.adjust: Adjusted p-value from the enrichment test

  • qvalue: Q-value from the enrichment test

  • geneID: Genes in the user list that are also in the gene set

  • Database: Name of the database