# scClassify: single-cell Hierarchical Classification

## Documentation for package ‘scClassify’ version 1.4.0

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

## Help Pages

.scClassifyTrainModel | The scClassifyTrainModel class
cellTypeTrain | Accessors of cellTypeTrain for scClassifyTrainModel
cellTypeTrain-method | Accessors of cellTypeTrain for scClassifyTrainModel
cellTypeTree | Accessors of cellTypeTree for scClassifyTrainModel
cellTypeTree-method | Accessors of cellTypeTree for scClassifyTrainModel
features | Accessors of features for scClassifyTrainModel
features-method | Accessors of features for scClassifyTrainModel
getN | Function to get the required N given by the accuracy and the learning curve model
learningCurve | Fit learning curve for accuracy matrix
model | Accessors of model for scClassifyTrainModel
model-method | Accessors of model for scClassifyTrainModel
modelweights | Accessors of modelweights for scClassifyTrainModel
modelweights-method | Accessors of modelweights for scClassifyTrainModel
name | Accessors of name for scClassifyTrainModel
name-method | Accessors of name for scClassifyTrainModel
plotCellTypeTree | To plot cell type tree
predict_scClassify | Testing scClassify model
predict_scClassifyJoint | Testing scClassify model (joint training)
runHOPACH | Create HOPACH tree
runSampleCal | Run sample size calculation for pilot data for reference dataset
scClassify | Train and test scClassify model
scClassifyTrainModel-class | An S4 class to stored training model for scClassify
scClassifyTrainModelList | The scClassifyTrainModelList class
scClassifyTrainModelList-class | An S4 class to stored a list of training models from scClassify
scClassify_example | Example data used in scClassify package
trainClassExample_wang | Subset of pretrained model of Wang et al.
trainClassExample_xin | Subset of pretrained model of Xin et al.
train_scClassify | Training scClassify model