Man pages for Militeee/rcongas
Copy Number Alterations genotyping from single-cell multiomics
| atac_counts | Example tibbles with input ATAC data in the format for... |
| auto_config_run | Determine data-based hyperparameters for the Bayesian priors. |
| auto_normalisation_factor | Compute empirical normalisation factors (library size) |
| build_clone_tree | Build Clone Tree form a CONGAS+ object Using medicc2 |
| campbell_bcpdx | Breast cancer patient-derived xenograft (10x RNA,... |
| change_spot | Add a deletion or an insertion in a given segment |
| create_congas_tibble | Format the input counts before creating the CONGAS+ object |
| create_df_from_range | Create a dataframe from a breakpoint list |
| divide_genome_in_segments | A simple function to divide the genome in segments |
| filter_cells_by_quantile | Filter cells by upper and lower quantile of their... |
| filter_counts_by_quantile | Filter observed counts by quantile. |
| filter_known_genes | Filter genes from an RNA tibble. |
| filter_missing_data | Filter per-segment outliers by quantiles. |
| filter_outliers | Filter per-segment outliers by quantiles. |
| filter_segments | Filter segments. |
| fit_congas | Fit an (R)CONGAS+ model |
| generate_cluster_ploidy_df | generate a dataframe with segments coordinates and... |
| generate_ploidy | Generete the ploidy for a segment |
| generate_ploidy_parent | Generat the ploidy given a parent clone |
| generate_ploidy_parent_fine | Generate the ploidy given a parent clone (with a finer... |
| generate_random_tree | Generate a random tree |
| get_fit | Extract fit data. |
| get_input | Extract input data. |
| hg38_karyo | Karyotype hg38 |
| init | Create a dataset. |
| metadata | Dataframe containing cell type annotations for the 10x... |
| multiome_congas_object | Multiome congas object |
| patel_gbmtn | Glioblastoma tumour and normal (SmartSeq RNA, z-score) |
| pipe | Pipe operator |
| plot_data | Plot data. |
| plot_fit | Plot fits. |
| plot.rcongasplus | Plot for an object of class "rcongasplus". |
| print.rcongasplus | Print for an object of class "rcongasplus". |
| randomize_breaks | Add stocasticity in the brakpoints |
| rna_counts | Example tibbles with input RNA data in the format for... |
| run_simulation | Run a complete simulation |
| segments_selector_congas | Filter segments where the optimal number of clusters is 1. |
| stat | Compute the statistics of a dataset. |
| zaho_hemato | Hematopoietic bone marrow failure (10x RNA, counts-based) |
