RT Journal Article
SR Electronic
T1 HieRFIT: Hierarchical Random Forest for Information Transfer
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.09.16.300822
DO 10.1101/2020.09.16.300822
A1 Yasin Kaymaz
A1 Florian Ganglberger
A1 Ming Tang
A1 Francesc Fernandez-Albert
A1 Nathan Lawless
A1 Timothy Sackton
YR 2020
UL http://biorxiv.org/content/early/2020/09/18/2020.09.16.300822.abstract
AB The emergence of single-cell RNA sequencing (scRNA-seq) has led to an explosion in novel methods to study biological variation among individual cells, and to classify cells into functional and biologically meaningful categories. Here, we present a new cell type projection tool, HieRFIT (Hierarchical Random Forest for Information Transfer), based on hierarchical random forests. HieRFIT uses a priori information about cell type relationships to improve classification accuracy, taking as input a hierarchical tree structure representing the class relationships, along with the reference data. We use an ensemble approach combining multiple random forest models, organized in a hierarchical decision tree structure. We show that our hierarchical classification approach improves accuracy and reduces incorrect predictions especially for inter-dataset tasks which reflect real life applications. We use a scoring scheme that adjusts probability distributions for candidate class labels and resolves uncertainties while avoiding the assignment of cells to incorrect types by labeling cells at internal nodes of the hierarchy when necessary. Using HieRFIT, we re-analyzed publicly available scRNA-seq datasets showing its effectiveness in cell type cross-projections with inter/intra-species examples. HieRFIT is implemented as an R package and it is available at (https://github.com/yasinkaymaz/HieRFIT/releases/tag/v1.0.0)Competing Interest StatementThe authors have declared no competing interest.