CoGAPS-package |
CoGAPS: Coordinated Gene Analysis Pattern Sets |
binaryA |
'binaryA' creates a binarized heatmap of the A matrix in which the value is 1 if the value in Amean is greater than threshold * Asd and 0 otherwise |
calcCoGAPSStat |
CoGAPS gene set statistic |
CoGAPS |
'CoGAPS' calls the C++ MCMC code through gapsRun and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix and then calls calcCoGAPSStat to estimate gene set activity with nPerm set to 500 |
computeGeneGSProb |
CoGAPS gene membership statistic |
gapsMapRun |
'gapsMapRun' calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix; as opposed to gapsRun, this method takes an additional input specifying set patterns in the P matrix |
gapsRun |
'gapsRun' calls the C++ MCMC code and performs Bayesian matrix factorization returning the two matrices that reconstruct the data matrix |
geneGSProb |
CoGAPS gene membership statistic |
GIST.D |
Sample GIST gene expression data from Ochs et al. (2009). |
GIST.S |
Sample GIST gene expression data from Ochs et al. (2009). |
GSets |
Simulated dataset to quantify gene set membership. |
plotAtoms |
'plotAtoms' a simple plot of the number of atoms from one of the vectors returned with atom numbers |
plotDiag |
'plotDiag' plots a series of diagnostic plots |
plotGAPS |
Plotter for GAPS decomposition results |
plotP |
'plotP' plots the P matrix in a line plot with error bars |
plotSmoothPatterns |
Plot loess smoothed CoGAPS patterns |
reorderByPatternMatch |
Match two sets of patterns found with CoGAPS |
residuals |
'residuals' calculate residuals and produce heatmap |
SimpSim.A |
Simulated data |
SimpSim.D |
Simulated data |
SimpSim.P |
Simulated data |
SimpSim.S |
Simulated data |
tf2ugFC |
Gene sets defined by transcription factors defined from TRANSFAC. |