formatGOdb: Creates a GO database compatible with topGO from .gaf file...
In oberstal/pfGO: Plasmodium falciparum functional enrichment analysis tools
formatGOdb R Documentation
Creates a GO database compatible with topGO from .gaf file retrieved from PlasmoDB.
Description
Fetches P. falciparum annotations from PlasmoDB, from which it creates a GO database compatible with topGO. The output can be used as the geneID2GO parameter for run.topGO.meta. A generally useful tool for keeping GO analyses up-to-date.
Usage
formatGOdb(url, organism = "Pf", plasmoDB_version = "")
Arguments
url
= url or filepath to a .gaf or gz-compressed gaf file. Defaults to latest Pf consortium .gaf annotation file hosted at PlasmoDB: /urlhttps://plasmodb.org/common/downloads/Current_Release/Pfalciparum3D7/gaf/PlasmoDB-CURRENT_Pfalciparum3D7_GO.gaf.gzip. Note that zip archives won't work directly with this function. Zip files need to be downloaded and unzipped, then the 'url' argument should be updated to the local unzipped file path.
organism
= optional string to include in your output file-name. Defaults to "Pf".
plasmoDB_version
= optional string to include the PlasmoDB release version in your output filename (e.g. "v66").
Details
Outputs a dated file named "*_GOdb.out" to the ./Routput folder. ./Routput will be created if it doesn't already exist. Note that the PlasmoDB release version isn't recorded automatically in the filename, so it is good practice to include the current PlasmoDB release number in the filename via the 'organism' parameter for your records.
You will need to run topGO::readmappings() on the file generated with formatGOdb before using it as the geneID2GO parameter.
Example: geneID2GO <- topGO::readmappings("./Routput/Pf_Mar022022_GOdb.out")
Notes on .gaf format
The .gaf file should be in tabular format with 17 columns, one row for each GO term associated with a geneID. No formatting is necessary when using the provided url.
Retrieves GO annotations assigned by all evidence-codes. A version that weeds out any non-curated, Inferred-from-Electronic-Annotation assignments, Inferred from Biological aspect of Ancestor, or Nontraceable Author Statements is also included in this package (evidence codes IEA,IBA,NAS; see formatGOdb.curated)
a GOdb from PlasmoDB's P. falciparum annotation (from PlasmoDB release 66; accessed Sep 28, 2023) pre-formatted using the curated version of this function and ready for run.topGO.meta is included in this package (Pfal_geneID2GO_curated).
See Also
formatGOdb.curated()
oberstal/pfGO documentation built on April 22, 2024, 7:15 a.m.
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| formatGOdb | R Documentation |
Creates a GO database compatible with topGO from .gaf file retrieved from PlasmoDB.
Description
Fetches P. falciparum annotations from PlasmoDB, from which it creates a GO database compatible with topGO. The output can be used as the geneID2GO parameter for run.topGO.meta. A generally useful tool for keeping GO analyses up-to-date.
Usage
formatGOdb(url, organism = "Pf", plasmoDB_version = "")
Arguments
url |
= url or filepath to a .gaf or gz-compressed gaf file. Defaults to latest Pf consortium .gaf annotation file hosted at PlasmoDB: /urlhttps://plasmodb.org/common/downloads/Current_Release/Pfalciparum3D7/gaf/PlasmoDB-CURRENT_Pfalciparum3D7_GO.gaf.gzip. Note that zip archives won't work directly with this function. Zip files need to be downloaded and unzipped, then the 'url' argument should be updated to the local unzipped file path. |
organism |
= optional string to include in your output file-name. Defaults to "Pf". |
plasmoDB_version |
= optional string to include the PlasmoDB release version in your output filename (e.g. "v66"). |
Details
Outputs a dated file named "*_GOdb.out" to the ./Routput folder. ./Routput will be created if it doesn't already exist. Note that the PlasmoDB release version isn't recorded automatically in the filename, so it is good practice to include the current PlasmoDB release number in the filename via the 'organism' parameter for your records.
You will need to run topGO::readmappings() on the file generated with formatGOdb before using it as the geneID2GO parameter.
Example: geneID2GO <- topGO::readmappings("./Routput/Pf_Mar022022_GOdb.out")
Notes on .gaf format
The .gaf file should be in tabular format with 17 columns, one row for each GO term associated with a geneID. No formatting is necessary when using the provided url.
Retrieves GO annotations assigned by all evidence-codes. A version that weeds out any non-curated, Inferred-from-Electronic-Annotation assignments, Inferred from Biological aspect of Ancestor, or Nontraceable Author Statements is also included in this package (evidence codes IEA,IBA,NAS; see formatGOdb.curated)
a GOdb from PlasmoDB's P. falciparum annotation (from PlasmoDB release 66; accessed Sep 28, 2023) pre-formatted using the curated version of this function and ready for run.topGO.meta is included in this package (Pfal_geneID2GO_curated).
See Also
formatGOdb.curated()
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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