makeGSEAplots


a numeric or integer vector of phenotypes in descending or ascending 
order with elements named by their Entrez IDs (no duplicates nor NA values)


geneList


a character vector of gene identifiers of a gene set


geneSet


a single integer or numeric value used in weighting phenotypes in GSEA 


exponent


a single character value specifying the directory where the GSEA plot 
will be stored


filepath


a single character value specifying the name of the file where the 
GSEA plot will be stored


filename


a single character value specifying the format of output image: "pdf" or
"png"


output


other arguments used by the function 'png' or 'pdf' such as width and height


internal

This package provides classes and methods for gene set
over-representation, enrichment and network analyses on
high-throughput screens. The over-representation analysis is
performed based on hypergeometric tests. The enrichment
analysis is based on the GSEA algorithm (Subramanian et al.
PNAS 2005). The network analysis identifies enriched
subnetworks based on algorithms from the BioNet package
(Beisser et al., Bioinformatics 2010). A pipeline is also
specifically designed for cellHTS2 object to perform
integrative network analyses of high-throughput RNA
interference screens. The users can build their own analysis
pipeline for their own data set based on this package.

Xin Wang

HTSanalyzeR

Gene set over-representation, enrichment and network analyses
for high-throughput screens

makeGSEAplots function

a numeric or integer vector of phenotypes in descending or ascending 
order with elements named by their Entrez IDs (no duplicates nor NA values)

a character vector of gene identifiers of a gene set

a single integer or numeric value used in weighting phenotypes in GSEA

a single character value specifying the directory where the GSEA plot 
will be stored

a single character value specifying the name of the file where the 
GSEA plot will be stored

a single character value specifying the format of output image: "pdf" or
"png"

other arguments used by the function 'png' or 'pdf' such as width and height

makeGSEAplots: Produce GSEA plots

Description

Usage

Arguments

Details