Function reference
Core Package Functions
Identifying marker genes, creating models, and classifying cells to a reference dataset.
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FindMarkerGenes() - Finds marker genes at each hierarchical level specified by the tree, using the GE matrix provided in the ref_bpcells parameter, and the celltype labels provided in the input to ref_metadata. It identifies marker genes by using a function provided in the BPCells package, marker_features, which finds genes using the Wilcoxon test.
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GetModels() - Function that gives models trained to differentiate all pairwise matchups.
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Classify() - Classification function that takes in input dataset (in BPCells format), alongside created models and the tree structure and provides a vector of classifications.
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CreateHierarchy() - Create Hierarchical Tree Structure from CSV with parent and child nodes named in a csv file
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CreateEqualTree() - This function is meant for users who don't want to use the tree-based/hierarchical functionality of the package. It creates a tree that assumes that all the celltype labels are at the same level of the tree.
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test_ex_data_bpcells - PBMC 3k dataset subset
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test_ex_metadata - PBMC 3k dataset testing metadata
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train_ex_data_bpcells - PBMC 3k dataset subset
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train_ex_metadata - PBMC 3k dataset training metadata