diff --git a/docs/merged_objects.md b/docs/merged_objects.md index d9a9775c..d428b86b 100644 --- a/docs/merged_objects.md +++ b/docs/merged_objects.md @@ -77,7 +77,7 @@ The following per-cell data columns are included for each cell, calculated using | `submitter_celltype_annotation` | If available, cell type annotations obtained from the group that submitted the original data. Cells that the submitter did not annotate are labeled as `"Submitter-excluded"` | | `singler_celltype_annotation` | If cell typing with `SingleR` was performed, the annotated cell type. Cells labeled as `NA` are those which `SingleR` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"` | | `singler_celltype_ontology` | If cell typing with `SingleR` was performed with ontology labels, the annotated cell type's ontology ID. Cells labeled as `NA` are those which `SingleR` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"` | -| `cellassign_celltype_annotation` | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"`. If `CellAssign` was unable to complete successfully for a given library, cells will be labeled as `Not run` | +| `cellassign_celltype_annotation` | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If cell typing was performed for some but not all libraries in the merged object, libraries without annotations will be labeled `"Cell type annotation not performed"`. If `CellAssign` was unable to complete successfully for a given library, cells will be labeled as `"Not run"` | | `cellassign_max_prediction` | If cell typing with `CellAssign` was performed and completed successfully, the annotation's prediction score (probability) | @@ -295,6 +295,7 @@ The columns `mean-SCPCL000000` and `detected-SCPCL000000` are present for each l | Column name | Contents | | ----------- | -------------------------------------------------------------- | +| `adt_id` | Name or ID of the ADT | | `mean-SCPCL000000` | Mean ADT count across all cells/droplets. Only present for libraries with CITE-seq data | | `detected-SCPCL000000` | Percent of cells in which the ADT was detected (ADT count > 0 ). Only present for libraries with CITE-seq data | | `target_type` | Whether each ADT is a target (`target`), negative/isotype control (`neg_control`), or positive control (`pos_control`). If this information was not provided, all ADTs will have been considered targets and will be labeled as `target` | diff --git a/docs/sce_file_contents.md b/docs/sce_file_contents.md index a488b7a2..74acb214 100644 --- a/docs/sce_file_contents.md +++ b/docs/sce_file_contents.md @@ -89,7 +89,7 @@ Further, if cell type annotation was performed, there will be additional columns | `cluster` | Cell cluster identity identified by graph-based clustering | | `singler_celltype_annotation` | If cell typing with `SingleR` was performed, the annotated cell type. Cells labeled as `NA` are those which `SingleR` could not confidently annotate | | `singler_celltype_ontology` | If cell typing with `SingleR` was performed with ontology labels, the annotated cell type's ontology ID. Cells labeled as `NA` are those which `SingleR` could not confidently annotate | -| `cellassign_celltype_annotation` | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If `CellAssign` was unable to complete successfully, cells will be labeled as `Not run` | +| `cellassign_celltype_annotation` | If cell typing with `CellAssign` was performed, the annotated cell type. Cells labeled as `"other"` are those which `CellAssign` could not confidently annotate. If `CellAssign` was unable to complete successfully, cells will be labeled as `"Not run"` | | `cellassign_max_prediction` | If cell typing with `CellAssign` was performed and completed successfully, the annotation's prediction score (probability) | ### SingleCellExperiment gene information and metrics @@ -260,6 +260,7 @@ This data frame contains the following columns with statistics for each ADT: | Column name | Contents | | ----------- | -------------------------------------------------------------- | +| `adt_name` | Name or ID of the ADT | | `mean` | Mean ADT count across all cells/droplets | | `detected` | Percent of cells in which the ADT was detected (ADT count > 0 ) | | `target_type` | Whether each ADT is a target (`target`), negative/isotype control (`neg_control`), or positive control (`pos_control`). If this information was not provided, all ADTs will have been considered targets and will be labeled as `target` |