process_GMT: Import and process GMT file.
In laurabiggins/GOcategoryStats: Provides statistics for Gene Ontology categories (Title Case)
Description
Usage
Arguments
Details
Value
Examples
View source: R/process_files.r
Description
Import GMT file containing gene sets.
Usage
1
process_GMT(file, min_genes = 3, max_genes = 5000)
Arguments
file
file path for gmt file containing gene sets
min_genes
minimum number of genes required in the functional category for the category to be loaded.
max_genes
maximum number of genes required in the functional category for the category to be loaded.
Details
The GMT format is described GMT format.
The first column should contain gene set names, the 2nd column contains a brief description and the 3rd column contains a whitespace separated list of genes.
Value
A named list containing all the gene sets imported from gmt_file_path
Examples
1
2
file <- "http://download.baderlab.org/EM_Genesets/current_release/Mouse/symbol/Mouse_GO_AllPathways_no_GO_iea_December_01_2018_symbol.gmt"
x <- process_GMT(file, 5, 5000)
laurabiggins/GOcategoryStats documentation built on Oct. 27, 2019, 11:36 a.m.
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Description Usage Arguments Details Value Examples
View source: R/process_files.r
Description
Import GMT file containing gene sets.
Usage
1 | process_GMT(file, min_genes = 3, max_genes = 5000)
|
Arguments
file |
file path for gmt file containing gene sets |
min_genes |
minimum number of genes required in the functional category for the category to be loaded. |
max_genes |
maximum number of genes required in the functional category for the category to be loaded. |
Details
The GMT format is described GMT format. The first column should contain gene set names, the 2nd column contains a brief description and the 3rd column contains a whitespace separated list of genes.
Value
A named list containing all the gene sets imported from gmt_file_path
Examples
1 2 | file <- "http://download.baderlab.org/EM_Genesets/current_release/Mouse/symbol/Mouse_GO_AllPathways_no_GO_iea_December_01_2018_symbol.gmt"
x <- process_GMT(file, 5, 5000)
|
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.
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