Man pages for rafalab/smallcount
Methods for Small Counts Stored in a Sparse Matrix
| CountTransform | CountTransform Constructor |
| CountTransform-class | Preprocessing Transformations on Sparse Count Matrices |
| cpm_log1p_transform | CPM Log1p Transformation |
| dot-calculateMu | Calculate mu values from row rates and column sums |
| dot-colsumsWithDefault | Return a non-null default value or compute column sums |
| dot-computePca | Compute the eigendecomposition of 'R %*% t(R)' for a residual... |
| dot-convertToSparse | Convert a sparse matrix to a SparseMatrix object |
| dot-nzcols | Get the column indices of non-zero matrix values |
| dot-nzrows | Get the row indices of non-zero matrix values |
| dot-poissonDevianceResidualsPca | Principal component analysis on deviance residuals |
| dot-poissonPearsonResidualsPca | Principal component analysis on Pearson residuals |
| dot-rawResidualsPca | Principal component analysis on raw residuals |
| dot-rowRatesWithDefault | Return a non-null default value or compute row-wise rates |
| groupRates | Row-wise Rates for Groups |
| identity_transform | Identity Transformation |
| log1p_transform | Log1p Transformation |
| poissonDeviance | Poisson Deviance |
| poissonDispersion | Poisson Dispersion |
| poissonPca | Principal Component Analysis on Poisson data |
| readSparseMatrix | Load data from a 10X Genomics experiment |
| scaled_log1p_transform | Scaled Log1p Transformation |
| tenx_subset | Compressed TENx brain data subset, genes in rows |
| TransformedMatrix | TransformedMatrix Constructor. |
| TransformedMatrix-class | Transformed Count Matrix |
| unzip_file | Decompress (and untar) .(t)gz or .(t)bz2 sparse matrix data... |
| validate_sample | Check that a path is a valid file, file directory, or file... |
