phantom (version 0.1.3)

run.phantom: Run phantom analysis

Description

This function allows user to run individual geneset heterogeneity analysis with phantom

Usage

run.phantom(data = NULL, geneset_list = NULL, query_geneset = NULL,
  ncluster = 2, nsample = 1000)

Arguments

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.

Examples

# NOT RUN {
## 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)
# }