Package 'enrichR'

Title: Provides an R Interface to 'Enrichr'
Description: Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See <https://maayanlab.cloud/Enrichr/> for further details.
Authors: Wajid Jawaid [aut, cre]
Maintainer: Wajid Jawaid <[email protected]>
License: GPL (>=2)
Version: 3.4
Built: 2025-02-02 22:21:05 UTC
Source: https://github.com/wjawaid/enrichR

Help Index

Upload background list using Speedrichr API

Description

Upload background list using Speedrichr API

Usage

.add_background(genes)

Arguments

genes

gene list

Details

Upload background list using Speedrichr API

Value

R object from JSON

Author(s)

I-Hsuan Lin [email protected]

Upload gene list using Speedrichr API

Description

Upload gene list using Speedrichr API

Usage

.add_list(genes)

Arguments

genes

Input genes

Details

Upload gene list using Speedrichr API

Value

R object that corresponds to the JSON object

Author(s)

I-Hsuan Lin [email protected]

Given a Enrichr output, order and subset criteria, returns a data frame accordingly

Description

Given a Enrichr output, order and subset criteria, returns a data frame accordingly

Usage

.enrichment_prep_df(df, showTerms = 20, orderBy = "P.value")

Arguments

df

Enrichr output
showTerms

Number of terms to show. Default 20.
orderBy

Column for ordering. Default "P.value"

Details

Given a Enrichr output, order and subset criteria, returns a data frame accordingly

Value

Data frame

Author(s)

I-Hsuan Lin [email protected]

FormatGenes

Description

Given an input, check format and return a character vector

Usage

.formatGenes(x, type = c("standard", "background"))

Arguments

x

Vector or dataframe of genes with or without score
type

Depends on type of gene input

Details

In standard analysis without background, crisp (symbols only) and fuzzy (with scores) gene sets are acceptable In analysis with background, only crisp gene sets are acceptable

Value

Character vector

Author(s)

I-Hsuan Lin [email protected]

Get enrichment result using Speedrichr API

Description

Get enrichment result using Speedrichr API

Usage

.get_backgroundenrich(uId, bId, db)

Arguments

uId

user List ID
bId

background ID
db

background Type

Details

Get enrichment result using Speedrichr API

Value

R object from JSON

Author(s)

I-Hsuan Lin [email protected]

onLoad hook to setup package options

Description

onLoad hook to setup package options

Usage

.onAttach(libname, pkgname)

Arguments

libname

(Required). Library name
pkgname

(Required). Package name

Details

onLoad hook to setup package options and to check connection to website

Author(s)

Wajid Jawaid [email protected]

Internal function to check RCurlOptions

Description

Internal function to check RCurlOptions

Usage

.proxyOpts()

Details

Internal function to check RCurlOptions

Value

Named vector

Author(s)

I-Hsuan Lin [email protected]

Download and parse GMT files from Enrichr

Description

Download and parse GMT files from Enrichr

Usage

.read_gmt(db)

Arguments

db

library

Details

Download and parse GMT files from Enrichr

Value

List object

Author(s)

I-Hsuan Lin [email protected]

Example background genes

Description

This is a character vector which consists of 20,625 gene symbols taken from the Enrichr website.

Usage

data(background)

Format

vector

Examples

data(background)
length(background)

Gene enrichment using Enrichr

Description

Gene enrichment using Enrichr

Usage

enrichr(
  genes,
  databases = NULL,
  background = NULL,
  include_overlap = FALSE,
  sleepTime = 1
)

Arguments

genes

(Required). Character vector of Entrez gene symbols as input. A data.frame of gene symbols in first column is also acceptable, optionally a score denoting the degree of membership between 0 and 1 in the second column.
databases

(Required). Character vector of databases to search. See https://maayanlab.cloud/Enrichr/ for available databases.
background

(Optional). Character vector of Entrez gene symbols to be used as background. A data.frame of gene symbols in first column is also acceptable. Default is "NULL". Enrichment analysis with background genes is only available on the main site (Enrichr). Also, it is using a different API service (Speedrichr), hence it is a little slower to complete and return the results.
include_overlap

(Optional). Download database in GMT format to include 'Overlap' in the resulting data.frame when analysing with a background. Default is "FALSE".
sleepTime

(Optional) Time to wait (in seconds) between sending requests to the server to prevent the same results being returned as the previous request. Default is 1.

Details

Gene enrichment using Enrichr, also, you can now try adding a background.

Value

Returns a list of data.frame of enrichment terms, p-values, ...

Author(s)

Wajid Jawaid [email protected]

Examples

# data(input) # Load example input genes
# data(background) # Load example background genes
# dbs <- c("GO_Molecular_Function_2023", "GO_Cellular_Component_2023",
#          "GO_Biological_Process_2023")
# if (getOption("enrichR.live")) {
#   enriched1 <- enrichr(input, dbs)
#   print(head(enriched1[[1]]))

#   # Include background
#   enriched2 <- enrichr(input, dbs, background = background)
#   print(head(enriched2[[1]]))

#   # Include background and add 'Overlap' info
#   enriched3 <- enrichr(input, dbs, background = background, include_overlap = TRUE)
#   print(head(enriched3[[1]]))
# }

790 gene symbols

Description

This is a character vector which consists of randomly selected 790 genes.

Usage

data(genes790)

Format

vector

Examples

data(genes790)
length(genes790)

Helper function for HTTP methods GET and POST

Description

Helper function

Usage

getEnrichr(method = "GET", url, ...)

Arguments

method

(Required). HTTP method. Default is "GET"
url

(Required). URL address requested
...

(Optional). Additional parameters to pass to GET

Details

Helper function for HTTP methods GET and POST

Value

same as GET

Author(s)

Wajid Jawaid [email protected]

I-Hsuan Lin [email protected]

Example input genes

Description

This is a character vector which consists of 375 gene symbols taken from the Enrichr website.

Usage

data(input)

Format

vector

Examples

data(input)
length(input)

Look up available databases on Enrichr

Description

Look up available databases on Enrichr

Usage

listEnrichrDbs()

Details

Look up available databases on Enrichr

Value

A data.frame of available Enrichr databases

Author(s)

Wajid Jawaid [email protected]

Examples

dbs <- listEnrichrDbs()

List Enrichr Websites

Description

List modEnrichr Websites

Usage

listEnrichrSites()

Details

List Enrichr Websites

Value

print Enrichr Website status

Author(s)

Alexander Blume

plotEnrich

Description

Visualise a Enrichr output as barplot

Usage

plotEnrich(
  df,
  showTerms = 20,
  numChar = 40,
  y = "Count",
  orderBy = "P.value",
  xlab = NULL,
  ylab = NULL,
  title = NULL
)

Arguments

df

(Required). A single data.frame from a list of Enrichr output.
showTerms

(Optional). Number of terms to show. Default is 20.
numChar

(Optional). A single integer. Default is 40. Indicates the number characters to keep in the term description.
y

(Optional). A character string. Default is "Count". Indicates the variable that should be mapped to the y-axis. It can be either "Count" or "Ratio". Results that includes background genes in the analysis can only show "Count".
orderBy

(Optional). A character string. Default is "P.value". Indicates how to order the Enrichr results before subsetting to keep top N terms. It can be one of these:

  • "P.value"

  • "Adjusted.P.value" (or "FDR")

  • "Combined.Score" (or "Score")

xlab

(Optional). A character string. Default is NULL. Indicates the x-axis label.
ylab

(Optional). A character string. Default is NULL. Indicates the y-axis label.
title

(Optional). A character string. Default is NULL Indicates the main title for the graphic.

Details

Visualise Enrichr result from a selected gene-set library as barplot.

Value

A ggplot plot object

Author(s)

I-Hsuan Lin [email protected]

See Also

ggplot

Examples

# data(input) # Load example input genes
# dbs <- c("GO_Molecular_Function_2023", "GO_Cellular_Component_2023",
#          "GO_Biological_Process_2023")
# if (getOption("enrichR.live")) {
#   enriched <- enrichr(input, dbs)
#   print(head(enriched[[1]]))
#   # Plot top 20 terms from "GO_Biological_Process_2023" and ordered by P-value
#   plotEnrich(enriched[[3]], showTerms = 20, numChar = 50, y = "Count",
#              orderBy = "P.value")
# }

printEnrich

Description

Print Enrichr results

Usage

printEnrich(
  data,
  prefix = "enrichr",
  showTerms = NULL,
  columns = c(1:9),
  outFile = c("txt", "excel")
)

Arguments

data

(Required). Output list object from the "enrichr" function.
prefix

(Optional). Prefix of output file. Default is "enrichr".
showTerms

(Optional). Number of terms to show. Default is NULL to print all terms.
columns

(Optional). Columns from each entry of data. Default is c(1:9) to print all columns. * Results without background: 1-"Term", 2-"Overlap", 3-"P.value", 4-"Adjusted.P.value", 5-"Old.P.value", 6-"Old.Adjusted.P.value", 7-"Odds.Ratio", 8-"Combined.Score", 9-"Combined.Score". * In results with background, the second column is "Rank" if terms are not identical with those annotated in the Enrichr GMT files
outFile

(Optional). Output file format, choose from "txt" and "excel". Default is "txt".

Details

Print Enrichr results from the selected gene-set libraries to individual text files or a Excel spreadsheet.

Author(s)

Wajid Jawaid [email protected]

I-Hsuan Lin [email protected]

Examples

# data(input) # Load example input genes
# if (getOption("enrichR.live")) {
#   enrichRLive <- TRUE
#   dbs <- listEnrichrDbs()
#   if(is.null(dbs)) enrichRLive <- FALSE
#   dbs <- c("GO_Molecular_Function_2023", "GO_Cellular_Component_2023",
#            "GO_Biological_Process_2023")
#   enriched <- enrichr(input, dbs)
#   print(head(enriched[[1]]))
#   # if (enrichRLive) printEnrich(enriched, outFile = "excel")
# }

Set Enrichr Website

Description

Set Enrichr Website

Usage

setEnrichrSite(site)

Arguments

site

site requested

Details

Set Enrichr Website

Value

Changes Enrichr Website connection

Author(s)

Alexander Blume