Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells


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Documentation for package ‘ADAPTS’ version 0.9.26

Help Pages

AugmentSigMatrix Make an augmented signature matrix
buildSpilloverMat Build a spillover matrix
clustWspillOver Cluster with spillover
collapseCellTypes Collapse cell yypes
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
getLM22cells LM22 look up table
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
MGSM27 Myeloma Genome Signature Matrix 27
missForest.par Use parallel missForest to impute missing values.
rankByT Rank genes for each cell type
remakeLM22p Make an Augmented Signature Matrix
spillToConvergence Spillover to convergence
SVMDECON Support vector machine deconvolution
weightNorm SVMDECONV helper function