Man pages for ADAPTS
Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells
| AugmentSigMatrix | Make an augmented signature matrix |
| buildSeed | Build a deconvolution seed matrix, add the proportional... |
| buildSpilloverMat | Build a spillover matrix |
| calcAcc | Calculate prediction accuracy |
| clustWspillOver | Cluster with spillover |
| collapseCellTypes | Collapse cell types |
| estCellCounts.nPass | Deconvolve with an n-pass spillover matrix |
| estCellPercent | Wrapper for deconvolution methods |
| estCellPercent.DCQ | DCQ Deconvolution |
| estCellPercent.DeconRNASeq | DeconRNASeq deconvolution |
| estCellPercent.nnls | Non-negative least squares deconvolution |
| estCellPercent.proportionsInAdmixture | WGCNA::proportionsInAdmixture deconvolution |
| estCellPercent.spillOver | Estimate cell percentage from spillover |
| estCellPercent.svmdecon | SVMDECON deconvolution |
| findConvergenceIter | Find out at which iteration the results converge, i.e. the... |
| getF1mcc | Get f1 / mcc |
| getLM22cells | LM22 look up table |
| gListFromRF | Build a gList using random forest |
| hierarchicalClassify | Hierarchical Deconvolution |
| hierarchicalSplit | Build hierarchical cell clusters. |
| licenses | Licenses required by Celgene legal |
| LM22 | Leukocyte 22 data matrix |
| loadMGSM27 | Load MGSM27 |
| loadModMap | LM22 to xCell LUT |
| loopTillConvergence | Loop testAllSigMatrices until convergence |
| matrixToGenelist | Make a GSVA genelist |
| meanResults | A meta analysis for the results from multiple iterations |
| MGSM27 | Myeloma Genome Signature Matrix 27 |
| missForest.par | Use parallel missForest to impute missing values. |
| plotKappas | Plot condition numbers |
| rankByT | Rank genes for each cell type |
| remakeLM22p | Make an Augmented Signature Matrix |
| scSample | Build groupSize pools according to cellIDs |
| shrinkByKappa | Calculate conditions numbers for signature subsets |
| shrinkSigMatrix | Shrink a signature matrix |
| spillToConvergence | Spillover to convergence |
| splitSCdata | Split a single cell dataset into multiple sets |
| SVMDECON | Support vector machine deconvolution |
| testAllSigMatrices | Generate all the signature matrices one time with the option... |
| weightNorm | SVMDECONV helper function |
