Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells

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Documentation for package ‘ADAPTS’ version 1.0.22

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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