Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

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Documentation for package ‘ADAPTS’ version 1.0.6

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
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