read.gmt: Read in gene set information from .gmt files
In arcolombo/junk: qusage: Quantitative Set Analysis for Gene Expression
Description
Usage
Arguments
Details
Value
Warning
Description
This function reads in and parses information from the MSigDB's .gmt files. Pathway information will be returned as a list of gene sets.
Usage
1
Arguments
file
The .gmt file to be read
Details
The .gmt format is a tab-delimited list of gene sets, where each line is a separate gene set. The first column must specify the name of the gene set, and the second column is used for a short description (which this function discards). For complete details on the .gmt format, refer to the Broad Institute's Data Format's page (url: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats).
Value
A list, where each index represents a separate gene set.
Warning
The function does not check that the file is correctly formatted, and may return incorrect or partial gene sets, e.g. if the first two columns are omitted. Please make sure that files are correctly formatted before reading them in using this function.
arcolombo/junk documentation built on May 10, 2019, 12:49 p.m.
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Description Usage Arguments Details Value Warning
Description
This function reads in and parses information from the MSigDB's .gmt files. Pathway information will be returned as a list of gene sets.
Usage
1 |
Arguments
file |
The .gmt file to be read |
Details
The .gmt format is a tab-delimited list of gene sets, where each line is a separate gene set. The first column must specify the name of the gene set, and the second column is used for a short description (which this function discards). For complete details on the .gmt format, refer to the Broad Institute's Data Format's page (url: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats).
Value
A list, where each index represents a separate gene set.
Warning
The function does not check that the file is correctly formatted, and may return incorrect or partial gene sets, e.g. if the first two columns are omitted. Please make sure that files are correctly formatted before reading them in using this function.
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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