makeOverlapTable


a character vector of gene identifiers specifying a gene set


geneSet


a character vector of gene identifiers specifying all hits in the screen


hits


a list of targeting identifiers with a name for each entry of the list 
as the identifier to be mapped


mapID


a single character value specifying the directory where the overlapped 
gene list will be stored


filepath


a single character value specifying the name of the file where the 
overlapped gene list will be stored


filename

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

makeOverlapTable function

a character vector of gene identifiers specifying a gene set

a character vector of gene identifiers specifying all hits in the screen

a list of targeting identifiers with a name for each entry of the list 
as the identifier to be mapped

a single character value specifying the directory where the overlapped 
gene list will be stored

a single character value specifying the name of the file where the 
overlapped gene list will be stored

makeOverlapTable: Find and save the overlapped genes between a gene set and a vector of hits

Description

Usage

Arguments

Details