run.phantom.batch: Run phantom batch analysis

In phantom: Gene Set Pareto Heterogeneity Analysis of Time-Course Gene Expression Data

Description

This function allows user to run batch analysis of a full geneset list with phantom, and download the identified heterogeneous genesets

Usage

run.phantom.batch(data = NULL, geneset_list = NULL, maxncluster = 5,
  nsample = 1000, report_pval = 0.05, report_nmin = 5,
  output_dir = file.path("./phantom_result"))

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)
maxncluster	The maximum number of clusters within a geneset user wants to test with. All numbers from 1 to ncluster will be tested and an optimal cluster number will be selected 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.
report_pval	The maximum p value of a geneset that will be reported as a significant heterogeneous geneset. Genesets with p value larger than report_pval wil not be reported
report_nmin	The minmum size of subcluster in a geneset that will be reported as a significant heterogeneous geneset.
output_dir	The directory where user wants to put the phantom batch analysis results

Examples

## load in the demo data and geneset in phantom package
data("time.course.data")
data("kegg.geneset")

## store the analysis result in an object
## Not run: obj = run.phantom.batch(data = time.course.data, geneset_list = kegg.geneset,
                  maxncluster = 5, nsample = 1000, report_pval = 0.05, report_nmin = 5,
                  output_dir = file.path(getwd(),'/phantom_result'))
## End(Not run)

phantom documentation built on May 2, 2019, 6:01 a.m.