AddSickleJrMetadata |
Add metadata to an object of class SickleJr |
BuildKNNGraphLaplacians |
Build KNN graphs and generate their graph Laplacians |
BuildSNNGraphLaplacians |
Build SNN graphs and generate their graph Laplacians |
CalculateUMAPSickleJr |
Calculate the UMAP for an object of class SickleJr |
ClusterSickleJr |
Cluster the \mathbf{H} matrix |
CreateSickleJr |
Create an object of class SickleJr |
DetermineClusters |
Perform clustering diagnostics |
DetermineDFromIRLBA |
Create elbow plots of the singular values derived from IRLBA to determine D for large datasets |
GenerateWmatricesandHmatrix |
Initialize the \mathbf{W} matrices in each modality and the shared \mathbf{H} matrix |
jrSiCKLSNMF |
Run jrSiCKLSNMF outside of a SickleJr object |
MinibatchDiagnosticPlot |
Plot a diagnostic plot for the mini-batch algorithm |
NormalizeCountMatrices |
Normalize the count matrices and set whether to use the Poisson KL divergence or the Frobenius norm |
PlotLossvsLatentFactors |
Create plots to help determine the number of latent factors |
PlotSickleJrUMAP |
Generate UMAP plots for an object of class SickleJr |
RunjrSiCKLSNMF |
Run jrSiCKLSNMF on an object of class SickleJr |
SetLambdasandRowReg |
Set lambda values and type of row regularization for an object of class SickleJr |
SetWandHfromWHinitials |
Set \mathbf{W} matrices and \mathbf{H} matrix from pre-calculated values |
SickleJr |
The SickleJr class |
SickleJr-class |
The SickleJr class |
SimData |
A simulated dataset for use with jrSiCKLSNMF |
SimSickleJrSmall |
A small SickleJr object containing a subset of data from the SimData data object. Contains the completed analysis from the 'Getting Started' vignette for a small subset of 10 cells with 150 genes and 700 peaks. The clusters derived from this dataset are not accurate; this dataset is intended for use with code examples. |