minSetSize-methods: GeneSetCollection length filtering
In gCMAP: Tools for Connectivity Map-like analyses
Description
Usage
Arguments
Value
Author(s)
Examples
Description
This function filteres a GeneSetCollection by removing all contained
GeneSets that do not include at least the user-specified number of
genes also found in the user-specified universe.
Usage
1
2
## S4 method for signature 'CMAPCollection'
minSetSize(sets, universe=NULL, min.members = 5)
Arguments
sets
A CMAPCollection object.
universe
Optional character vector of gene identfiers to be considered as the
universe. Only geneIds included in the universe will count toward the
gene set membership counts. If 'NULL' (default), all featureNames of the
CMAPCollection will be considered.
min.members
Number of genes (in the univerese) a gene set needs to contain to be retained.
Value
A CMAPCollection with all gene sets containing more than the specified
number of members.
Author(s)
Thomas Sandmann
Examples
1
2
3
4
data(gCMAPData)
gene.set.collection <- induceCMAPCollection(gCMAPData, "z", higher=2, lower=-2)
minSetSize(gene.set.collection, min.members=100)
gCMAP documentation built on April 29, 2020, 3:54 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 Value Author(s) Examples
Description
This function filteres a GeneSetCollection by removing all contained GeneSets that do not include at least the user-specified number of genes also found in the user-specified universe.
Usage
1 2 | ## S4 method for signature 'CMAPCollection'
minSetSize(sets, universe=NULL, min.members = 5)
|
Arguments
sets |
A |
universe |
Optional character vector of gene identfiers to be considered as the universe. Only geneIds included in the universe will count toward the gene set membership counts. If 'NULL' (default), all featureNames of the CMAPCollection will be considered. |
min.members |
Number of genes (in the univerese) a gene set needs to contain to be retained. |
Value
A CMAPCollection with all gene sets containing more than the specified number of members.
Author(s)
Thomas Sandmann
Examples
1 2 3 4 | data(gCMAPData)
gene.set.collection <- induceCMAPCollection(gCMAPData, "z", higher=2, lower=-2)
minSetSize(gene.set.collection, min.members=100)
|
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.