genGenelists

list containing Biopax model with newly generated internal IDs
 as processed with genintIDs function.
The components of the list are biopax models for "biocarta", "kegg", "nci",
 "reactome". In case a database was not chosen the list
entry contains a NA.

intIDs

vector indicating with which pathway database the pathways
 should be determined; possible choices
are "biocarta", "kegg", "nci", "reactome".

pwdatabases


This function generates genelists from the chosen pathway databases for
further processing in detPathways function.


manip

pwOmics performs pathway-based level-specific data
comparison of matching omics data sets based on pre-analysed
user-specified lists of differential genes/transcripts and
proteins. A separate downstream analysis of proteomic data
including pathway identification and enrichment analysis,
transcription factor identification and target gene
identification is opposed to the upstream analysis starting
with gene or transcript information as basis for identification
of upstream transcription factors and regulators. The
cross-platform comparative analysis allows for comprehensive
analysis of single time point experiments and time-series
experiments by providing static and dynamic analysis tools for
data integration.

Astrid Wachter

pwOmics

Pathway-based data integration of omics data

genGenelists function

This function generates genelists from the chosen pathway databases for
further processing in detPathways function.

genGenelists: Generate genelists from pathway databases.

Description

Usage

Arguments

Value