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Type: Package
Title: Get Gene Sets for Gene Enrichment Analysis
Version: 0.2.7
Maintainer: Yunze Liu <jieandze1314@gmail.com>
URL: https://github.com/GangLiLab/geneset
BugReports: https://github.com/GangLiLab/geneset/issues
Description: Gene sets are fundamental for gene enrichment analysis. The package 'geneset' enables querying gene sets from public databases including 'GO' (Gene Ontology Consortium. (2004) <doi:10.1093/nar/gkh036>), 'KEGG' (Minoru et al. (2000) <doi:10.1093/nar/28.1.27>), 'WikiPathway' (Marvin et al. (2020) <doi:10.1093/nar/gkaa1024>), 'MsigDb' (Arthur et al. (2015) <doi:10.1016/j.cels.2015.12.004>), 'Reactome' (David et al. (2011) <doi:10.1093/nar/gkq1018>), 'MeSH' (Ish et al. (2014) <doi:10.4103/0019-5413.139827>), 'DisGeNET' (Janet et al. (2017) <doi:10.1093/nar/gkw943>), 'Disease Ontology' (Lynn et al. (2011) <doi:10.1093/nar/gkr972>), 'Network of Cancer Genes' (Dimitra et al. (2019) <doi:10.1186/s13059-018-1612-0>) and 'COVID-19' (Maxim et al. (2020) <doi:10.21203/rs.3.rs-28582/v1>). Gene sets are stored in the list object which provides data frame of 'geneset' and 'geneset_name'. The 'geneset' has two columns of term ID and gene ID. The 'geneset_name' has two columns of terms ID and term description.
License: GPL-3
Encoding: UTF-8
LazyData: true
Depends: R (≥ 3.6)
Imports: dplyr, RCurl, fst, stringi, stringr
RoxygenNote: 7.2.2
Suggests: testthat (≥ 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2022-11-20 06:26:48 UTC; reedliu1
Author: Yunze Liu ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2022-11-20 07:10:07 UTC

Datasets go_org contains GO species information

Description

Datasets go_org contains GO species information

Datasets kegg_org contains KEGG species information

Datasets wiki_org contains WikiPathway species information

Datasets msigdb_org contains Msigdb species information

Datasets enrichr_metadata contains Enrichrdb information

Datasets reactome_org contains Reactome species information

Datasets mesh_org contains MeSH species information

Datasets mesh_metadata contains MeSH information

Datasets org2cate contains all organism to category information

Datasets org2cate contains all organism to category information

Datasets ensOrg_name contains organism name of ensembl

Get EnrichrDB geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id

Description

Get EnrichrDB geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id

Usage

getEnrichrdb(
  org = c("human", "fly", "yeast", "worm", "zebrafish"),
  library = NULL,
  download.method = NULL,
  data_dir = NULL
)

Arguments

org

Organism from 'human','fly','yeast','worm','zebrafish'.

library

Choose one library name from 'enrichr_metadata'.

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset and geneset name.

Examples

x = getEnrichrdb(org = "human", library = "COVID-19_Related_Gene_Sets",
data_dir = tempdir())

Get GO geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Get GO geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Usage

getGO(
  org = "human",
  ont = c("bp", "cc", "mf"),
  download.method = NULL,
  data_dir = NULL
)

Arguments

org

Organism name from 'go_org'.

ont

One of "bp","cc" or "mf" ontology.

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset and geneset name.

Examples


x = getGO(org = "human",ont = "mf", data_dir = tempdir())

Get HgDisease geneset and geneset_name Human disease gene sets from Disease Ontology (DO),DisGeNET, Network of Cancer Gene (NCG) version 6 and v7, and covid19-specific. Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Get HgDisease geneset and geneset_name Human disease gene sets from Disease Ontology (DO),DisGeNET, Network of Cancer Gene (NCG) version 6 and v7, and covid19-specific. Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Usage

getHgDisease(
  source = c("do", "disgenet", "ncg_v7", "ncg_v6", "covid19"),
  download.method = NULL,
  data_dir = NULL
)

Arguments

source

Choose from 'do','ncg_v7','ncg_v6','disgenet','covid19'.

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list.

Examples


x = getHgDisease(source = "do", data_dir = tempdir())

Get KEGG geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Get KEGG geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Usage

getKEGG(
  org = "hsa",
  category = c("pathway", "module", "enzyme", "disease", "drug", "network"),
  download.method = NULL,
  data_dir = NULL
)

Arguments

org

Organism name from 'kegg_org'.

category

Choose one category from "pathway","module", "enzyme", 'disease' (human only),'drug' (human only) or 'network' (human only)

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset and geneset name.

Examples


x = getKEGG(org = "hsa",category = "pathway", data_dir = tempdir())

Get MeSH geneset and geneset_name MeSH is the annotation used for MEDLINE/PubMed articles and is manually curated by NLM (U.S. National Library of Medicine). Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Get MeSH geneset and geneset_name MeSH is the annotation used for MEDLINE/PubMed articles and is manually curated by NLM (U.S. National Library of Medicine). Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Usage

getMesh(
  org = "human",
  method = c("gendoo", "gene2pubmed", "RBBH"),
  category = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "Z"),
  download.method = NULL,
  data_dir = NULL
)

Arguments

org

Organism mesh_name from 'mesh_org'.

method

Method of mapping MeSH ID to gene ID. Choose one from "gendoo", "gene2pubmed" or "RBBH" (mainly for some minor species). See also 'mesh_metadata'.

category

MeSH descriptor categories from 'mesh_metadata' (refer to: https://wikipedia.org/wiki/List_of_MeSH_codes).

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset and geneset name.

Examples


x = getMesh(org = "human", method = "gendoo", category = "A", data_dir = tempdir())

Get MsigDb geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id

Description

Get MsigDb geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id

Usage

getMsigdb(
  org = "human",
  category = c("H", "C1", "C2-CGP", "C2-CP-BIOCARTA", "C2-CP-KEGG", "C2-CP-PID",
    "C2-CP-REACTOME", "C2-CP-WIKIPATHWAYS", "C3-MIR-MIRDB", "C3-MIR-MIR_Legacy",
    "C3-TFT-GTRD", "C3-TFT-TFT_Legacy", "C4-CGN", "C4-CM", "C5-GO-BP", "C5-GO-CC",
    "C5-GO-MF", "C5-HPO", "C6", "C7-IMMUNESIGDB", "C7-VAX", "C8"),
  download.method = NULL,
  data_dir = NULL
)

Arguments

org

Organism name from 'msigdb_org'.

category

Choose one of "H", "C1", "C2-CGP", "C2-CP-BIOCARTA", "C2-CP-KEGG", "C2-CP-PID", "C2-CP-REACTOME", "C2-CP-WIKIPATHWAYS", "C3-MIR-MIRDB","C3-MIR-MIR_Legacy", "C3-TFT-GTRD", "C3-TFT-TFT_Legacy","C4-CGN", "C4-CM", "C5-GO-BP", "C5-GO-CC", "C5-GO-MF","C5-HPO", "C6", "C7-IMMUNESIGDB", "C7-VAX", "C8" (refer to: http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp)

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset.

Examples


x = getMsigdb(org = "human", category = "H", data_dir = tempdir())

Get Reactome geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Get Reactome geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Usage

getReactome(org = "human", download.method = NULL, data_dir = NULL)

Arguments

org

Organism name from 'reactome_org'.

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset and geneset name.

Examples


x = getReactome(org = "human", data_dir = tempdir())

Get WikiPathway geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Description

Get WikiPathway geneset and geneset_name Geneset is a data.frame of 2 columns with term id and gene id; Geneset_name is a data.frame of 2 columns with term id and term description

Usage

getWiki(org = "human", download.method = NULL, data_dir = NULL)

Arguments

org

Organism name from 'wiki_org'.

download.method

"auto" (as default if NULL), "wininet" (for windows)

data_dir

data saving location, default is the package data directory

Value

A list including geneset and geneset name.

Examples


x = getWiki(org = "human", data_dir = tempdir())

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