# Adaptive Dropout Imputer (ADImpute)

## Documentation for package ‘ADImpute’ version 1.2.0

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

## Help Pages

ArrangeData | Data trimming
CenterData | Data centering
CheckArguments_Impute | Argument check to Impute()
ChooseMethod | Method choice per gene
Combine | Combine imputation methods
ComputeMSEGenewise | Computation of MSE per gene
CreateArgCheck | Argument check
CreateTrainData | Preparation of training data for method evaluation
DataCheck_Matrix | Data check (matrix)
DataCheck_Network | Data check (network)
DataCheck_SingleCellExperiment | Data check (SingleCellExperiment)
DataCheck_TrLength | Data check (transcript length)
demo_data | Small dataset for example purposes
demo_net | Small regulatory network for example purposes
demo_sce | Small dataset for example purposes
EvaluateMethods | Imputation method evaluation on training set
GetDropoutProbabilities | Get dropout probabilities
HandleBiologicalZeros | Get dropout probabilities
Impute | Dropout imputation using different methods
ImputeBaseline | Impute using average expression across all cells
ImputeDrImpute | Use DrImpute
ImputeNetParallel | Network-based parallel imputation
ImputeNetwork | Network-based imputation
ImputeNPDropouts | Helper function to PseudoInverseSolution_percell
ImputePredictiveDropouts | Helper function to PseudoInverseSolution_percell
ImputeSAVER | Use SAVER
MaskData | Masking of entries for performance evaluation
MaskerPerGene | Helper mask function
network.coefficients | Transcriptome wide gene regulatory network
NormalizeRPM | RPM normalization
NormalizeTPM | TPM normalization
PseudoInverseSolution_percell | Network-based parallel imputation - Moore-Penrose pseudoinversion
ReadData | Data read
ReturnChoice | Wrapper for return of EvaluateMethods()
ReturnOut | Wrapper for return of Impute()
SetBiologicalZeros | Set biological zeros
SplitData | Selection of samples for training
transcript_length | Table for transcript length calculations
WriteCSV | Write csv file
WriteTXT | Write txt file