# Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

## Documentation for package ‘ADAPTS’ version 1.0.22

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

AugmentSigMatrix | Make an augmented signature matrix
buildSeed | Build a deconvolution seed matrix, add the proportional option
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 mean results are stable.
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 to leave out half of the data as a test set
weightNorm | SVMDECONV helper function