duplicateRemover


a single named numeric or integer vector with gene identifiers as names


geneList


a single character value specifying the method to remove the duplicates 
(should the minimum, maximum or average observation for a same construct 
be kept). The current version provides "min" (minimum), "max" (maximum), 
"average" and "fc.avg" (fold change average). The minimum and maximum 
should be understood in terms of absolute values (i.e. min/max effect, 
no matter the sign). The fold change average method converts the fold 
changes to ratios, averages them and converts the average back to a 
fold change.


method


This function gets rid of the duplicates in a vector of phenotypes with 
gene identifiers as names. It is used to prepare the named vector of 
phenotypes for the over-representation and enrichment analysis.


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

duplicateRemover function

a single named numeric or integer vector with gene identifiers as names

a single character value specifying the method to remove the duplicates 
(should the minimum, maximum or average observation for a same construct 
be kept). The current version provides "min" (minimum), "max" (maximum), 
"average" and "fc.avg" (fold change average). The minimum and maximum 
should be understood in terms of absolute values (i.e. min/max effect, 
no matter the sign). The fold change average method converts the fold 
changes to ratios, averages them and converts the average back to a 
fold change.

This function gets rid of the duplicates in a vector of phenotypes with 
gene identifiers as names. It is used to prepare the named vector of 
phenotypes for the over-representation and enrichment analysis.

duplicateRemover: Remove duplicates in a named vector of phenotypes

Description

Usage

Arguments

Value

See Also

Examples