Fast Functions for Differential Expression using Wilcox and AUC
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Documentation for package ‘presto’ version 1.0.0
Help Pages
| collapse_counts | Collapse counts based on multiple categorical metadata columns |
| compute_hash | Compute unique hash for each row of data.frame |
| exprs | Small gene expression matrix |
| nnzeroGroups | nnzeroGroups |
| nnzeroGroups.dgCMatrix | nnzeroGroups |
| nnzeroGroups.matrix | nnzeroGroups |
| object_sce | SingleCellExperiment object with fake data |
| object_seurat | Seurat V3 object with fake data |
| presto | presto |
| pseudobulk_deseq2 | Pseudobulk DESeq2 |
| pseudobulk_one_vs_all | Pseudobulk one versus all |
| pseudobulk_pairwise | Pseudobulk pairwise |
| pseudobulk_within | Pseudobulk within |
| rank_matrix | rank_matrix |
| rank_matrix.dgCMatrix | rank_matrix |
| rank_matrix.matrix | rank_matrix |
| sumGroups | sumGroups |
| sumGroups.dgCMatrix | sumGroups |
| sumGroups.matrix | sumGroups |
| summarize_dge_pairs | Summarize differential gene expression pairs |
| top_markers | Get top n markers from wilcoxauc |
| top_markers_dds | Get top n markers from pseudobulk DESeq2 |
| wilcoxauc | Fast Wilcoxon rank sum test and auROC |
| wilcoxauc.default | Fast Wilcoxon rank sum test and auROC |
| wilcoxauc.Seurat | Fast Wilcoxon rank sum test and auROC |
| wilcoxauc.seurat | Fast Wilcoxon rank sum test and auROC |
| wilcoxauc.SingleCellExperiment | Fast Wilcoxon rank sum test and auROC |
| y | Group labels for observations in gene expression matrix |