Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq

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Documentation for package ‘countland’ version 0.1.2

• DESCRIPTION file.
• Package NEWS.

Help Pages

Center	Recapitulate Seurat centering scaled and transformed data
Cluster	Perform spectral clustering on dot products.
CountIndex	Internal function for calculating count index.
countland	Initialize a countland object from a dgCMatrix
countland-class	An S4 class to represent a countland object
Dot	Calculate pairwise dot products of counts between all cells.
Embed	Perform spectral embedding on dot products.
IMA	run integer matrix approximation
IMA_Compute_Init_Scaled	rescale if max val is above upper bound
IMA_init	function to initialize U, V, and Lambda
IMA_params	Parameter class for IMA
IMA_Update_Factor	Update factor matrix - see SUSTain code
listCols	Split dgCMatrix into column vectors.
Log	Recapitulate Seurat log transformation
Normalize	Recapitulate Seurat normalization
PlotEigengap	Plots eigenvalues to investigate the optimal number of clusters
PlotEmbedding	Plot cells using spectral embedding of dot products.
PlotGeneCounts	Generate a strip plot for counts across selected genes
PlotIMA	Plot cells using integer matrix approximation
PlotIMAElbow	Plot the difference between the observed and reconstructed count matrix using integer matrix approximation and a series of total features.
PlotMarker	Plot cell using spectral embedding and display counts in a given gene.
PlotSharedCounts	Plot cells using matrix of counts summed by clusters of genes.
PrintGeneNumber	Restore count matrix to original state
RankMarkerGenes	Rank the top marker genes for each cluster from spectral clustering.
RemoveEmpty	Internal function to remove empty columns and rows
RescaleVariance	Recapitulate Seurat scaling to unit variance
RestoreCounts	Restore count matrix to original state
RunIMA	Perform integer matrix approximation on count matrix.
ScikitManifoldSpectralEmbedding	Recapitulate scikit.manifold.spectral_embedding from python.
ScoreCells	Calculate several scores for counts across cells
ScoreGenes	Calculate several scores for count-based gene expression.
SharedCounts	Combine groups of genes with similar counts by clustering and summing.
Subsample	Subsample cells to a standard number of counts by randomly sampling observations without replacement.
SubsampleCol	Internal function for subsampling a column from a sparse matrix.
SubsetCells	Subsets cells using a vector of cell indices
SubsetGenes	Subsets genes using a vector of gene indices