readPathwayGMT: Read Pathway GMT File
In rWikiPathways: rWikiPathways - R client library for the WikiPathways API
Description
Usage
Arguments
Details
Value
References
See Also
Examples
View source: R/readPathwayGMT.R
Description
Reads a WikiPathways GMT file to produce a data frame of
pathway-gene associations useful in enrichment analyses and other
applications.
Usage
1
Arguments
file
Path to GMT file
Details
The returned data frame includes pathway name, version, identifier,
and organism. The gene content is provided as NCBI Entrez Gene identifiers.
The input file can be retrieved by using
downloadPathwayArchive(organism="Homo sapiens",format="gmt").
Value
Data frame of pathway-gene associations
References
Adapted from the generic GMT reader provided by clusterProfiler,
https://github.com/YuLab-SMU/clusterProfiler/blob/master/R/GMT.R
See Also
downloadPathwayArchive
Examples
1
readPathwayGMT(system.file("extdata","wikipathways-20201010-gmt-Homo_sapiens.gmt", package="rWikiPathways"))
rWikiPathways documentation built on Feb. 28, 2021, 2:01 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value References See Also Examples
View source: R/readPathwayGMT.R
Description
Reads a WikiPathways GMT file to produce a data frame of pathway-gene associations useful in enrichment analyses and other applications.
Usage
1 |
Arguments
file |
Path to GMT file |
Details
The returned data frame includes pathway name, version, identifier,
and organism. The gene content is provided as NCBI Entrez Gene identifiers.
The input file can be retrieved by using
downloadPathwayArchive(organism="Homo sapiens",format="gmt").
Value
Data frame of pathway-gene associations
References
Adapted from the generic GMT reader provided by clusterProfiler, https://github.com/YuLab-SMU/clusterProfiler/blob/master/R/GMT.R
See Also
downloadPathwayArchive
Examples
1 | readPathwayGMT(system.file("extdata","wikipathways-20201010-gmt-Homo_sapiens.gmt", package="rWikiPathways"))
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.