Man pages for wgmao/PLIER
Pathway-Level Information Extractor (PLIER): a generative model for gene expression data
| bloodCellMarkersIRISDMAP | Blood cell markers |
| canonicalPathways | Canonical Pathways |
| chemgenPathways | Chemgen Pathways |
| combinePaths | combines binary pathway matricies into one, rownames are... |
| commonRows | returns the row names in common |
| computeChat | Computes the ridge pseudo-inverse of the prior information... |
| CTNNB1mut | Immune Markers (Clinical Pathways) |
| DataSmooth | SVD based smoothing for single cell RNAseq data |
| getCutoff | get the p-value cutoff for a specific FDR |
| HCCData | Hepatocellular carcinoma (HCC) Data |
| immunePathways | Immune Pathways |
| ListPriors | ListPriors |
| mapPathway | Rename pathway matrix gene names. Useful for species... |
| nameB | names latent variables according to their pathway useage (if... |
| num.pc | estimates the number of 'significant' principle components... |
| oncogenicPathways | Oncogenic Pathways |
| PLIER | Main PLIER function |
| plierResToMarkers | Creates a binary cell-type marker matrix using prior results.... |
| PLIERsparse | sparse PLIER function (experimental) |
| plotMat | generic function to plot the non-zero elements of a sparse... |
| plotTopZ | visualize the top genes contributing to the LVs |
| plotTopZallPath | visualize the top genes contributing to the LVs similarily to... |
| plotU | plot the U matrix from a PLIER decomposition |
| projectPLIER | project a new dataset onto PLIER LVs |
| rotateSVD | rotate SVD to maximize the L1 of positive U values |
| rowNorm | z-score each row of the data |
| simpleDecomp | Main PLIER function |
| SPVs | Surrogate Proportion Variables |
| svmMarkers | Blood cell markers |
| vacData | Vaccination Data |
| VarianceExplained | VarianceExplained |
| xCell | xCell signature sets |
