Data mining of public microarray data through connections to the TranscriptomeBrowser database.

[Up] [Top]

Documentation for package ‘RTools4TB’ version 1.8.0

Help Pages

RTools4TB_1.1.4-package The RTools4TB package: data mining of public microarray data through connections to the TranscriptomeBrowser database.
annotationList The keywords used to get information about functional enrichment of transcriptional signatures.
clusterEisen Performs system call to the Cluster 3.0 program.
colorScale Calibration bar for color images
createGraph4BioC Creates a graph based on a request to the TrancriptomeBrowser database.
createSignatures4TB Creates a set of transcriptional signatures from a microarray dataset.
DBF Density-Based Filtering.
DBFMCL The "Density Based Filtering and Markov CLustering" algorithm (DBF-MCL).
DBFMCLresult Class to store DBFMCL results.
DBFMCLresult-class Class to store DBFMCL results.
doNormalScore Normal score transformation of a matrix.
doRankTransformation Rank transformation of a matrix.
getData4DBFMCL Fetch an expression matrix from a file or an ExpressionSet object
getExpressionMatrix A function to fetch an expression matrix from the TranscriptomeBrowser database.
getSignatures A function to retrieve transcriptional signature IDs from the TranscriptomeBrowser database (TBrowserDB).
getTBInfo Get information about an experiment or a platform.
heatmapFromCDT Reads a "cdt" file containing a set of transcriptional signatures and produces heatmaps.
matplotProfiles An internal plotting function based on the matplot function.
MCL Invokes the Markov CLustering algorithm (MCL).
plotGeneExpProfiles Visualization of transcriptional signature profiles.
RTools4TB The RTools4TB package: data mining of public microarray data through connections to the TranscriptomeBrowser database.
show-method Class to store DBFMCL results.
writeDBFMCLresult Writes the results of DBFMCL function onto disk.