| 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  [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())