Description Usage Arguments Examples
This function allows user to run individual geneset heterogeneity analysis with phantom
1 2 | run.phantom(data = NULL, geneset_list = NULL, query_geneset = NULL,
ncluster = 2, nsample = 1000)
|
data |
User provided time-course data loaded by load.data() |
geneset_list |
User provided genesets list loaded by load.geneset(). Phanotm package provids four geneset lists from different resources: kegg, reactome, emory geneset and baylor modules. These genesets can be obtained with data(), e.g. data(kegg.geneset) |
query_geneset |
The name of a geneset user wants to analysis. This geneset should be from the geneset_list designated by geneset_list parameter |
ncluster |
The number of clusters within a geneset user wants to use to identify the heterogeneity of this geneset. |
nsample |
The times of random sampling that is used to build the NULL distribution for parato front analysis. |
1 2 3 4 5 6 7 8 9 10 | ## load in the demo data in phantom package
data("time.course.data")
## store the analysis result in an object
## Not run:
obj = run.phantom(data = time.course.data, geneset_list = reactome.geneset,
query_geneset ='REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES',
ncluster = 2, nsample = 1000)
## End(Not run)
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