Man pages for cancerit/RCRISPR
R Functions for CRISPR-Related Analyses
| add_bagel_classifications | Add BAGEL classifications |
| add_pseudocount | Add pseudocount |
| average_guide_bfs | Get average sgRNA BF per gene |
| average_replicates | Average replicates |
| bagel_gene_infile_options | Optparse options for BAGEL |
| bagel_normalisation_options | Optparse options for output paths |
| bagel_normalise_counts | Normalise counts using BAGEL method. |
| basic_infile_options | Optparse options for basic input |
| basic_outfile_options | Optparse options for basic output |
| calculate_gene_lfc | Calculate gene log fold changes. |
| calculate_gini_index | Calculate gini index |
| calculate_lfc | Calculate log fold changes. |
| calculate_lfc_options | Optparse options for output paths |
| check_dataframe | Check dataframe is not empty and indices are valid |
| check_directory | Run basic checks on directory |
| check_file | Run basic checks on input file |
| check_is_numeric_and_is_integer | Check value is numeric and is an integer. |
| check_option | Check optparse option is not null |
| compare_annotations | Compare annotations between two dataframes. |
| compare_count_matrix_to_library | Compare count matrix to LibraryAnnotation. |
| compare_counts_to_library | Compare SampleCounts to LibraryAnnotation. |
| compare_matrix_to_sample_metadata | Compare matrix to SampleMetadata. |
| convert_sample_counts_objects_to_count_matrix | Convert SampleCounts objects into count matrix. |
| convert_variable_to_integer | Converts variable value to integers |
| convert_variable_to_numeric | Converts variable value to numerics |
| correlation_options | Optparse options for sample correlations |
| count_column_index_options | Optparse options for count column indices |
| count_format_options | Optparse options for count formatting |
| count_library_outfile_options | Optparse options for count and library output paths |
| count_matrix_stats | Build count matrix statistics |
| count_path_options | Optparse options for count paths |
| counts | Generic for counts method |
| count_skip_options | Optparse options for skipping lines when reading files |
| counts-SampleCounts-method | Get counts from SampleCounts object |
| count_type_options | Optparse options for input count type |
| crisprcleanr_correction_options | Optparse options for CRISPRcleanR normalisation |
| crisprcleanr_normalisation_options | Optparse options for CRISPRcleanR normalisation |
| crisprcleanr_output_options | Optparse options for CRISPRcleanR outputs |
| duplicate_guide_options | Optparse options for output paths |
| filter_by_index_options | Optparse options for filtering data by index |
| filtered_guide_output_options | Optparse options for raw guide filter output |
| fold_change_column_index_options | Optparse options for fold change column indices |
| fold_change_format_options | Optparse options for count formatting |
| fold_change_path_options | Optparse options for fold change paths |
| gene_summary_top_n_genes | Retrieve top n genes from MAGeCK gene summary |
| get_bagel_statistics | Prepare BAGEL statistics |
| get_column_indices | Converts variable value to numerics |
| get_file_class | Get file class |
| get_guides_failing_filter | Identify guides failing count filter. |
| get_guides_with_no_coordinates | Identify guides with no coordinates from library annotation... |
| get_library_annotations | Generic for get_library_annotations method |
| get_library_annotations-LibraryAnnotations-method | Get library annotations from LibraryAnnotations object |
| get_mageck_gene_summary | Generic for get_mageck_gene_summary method |
| get_mageck_gene_summary-MageckGeneRRA-method | Get gene summary from MageckGeneRRA object |
| get_mageck_sgrna_gene_results | Generic for get_mageck_sgrna_gene_results method |
| get_mageck_sgrna_gene_results-MageckSgrnaRRA-method | Get sgRNA gene results from MageckSgrnaRRA object |
| get_mageck_sgrna_summary | Generic for get_mageck_sgrna_summary method |
| get_mageck_sgrna_summary-MageckSgrnaRRA-method | Get sgRNA summary from MageckSgrnaRRA object |
| get_sample_metadata | Generic for get_sample_metadata method |
| get_sample_metadata-SampleMetadata-method | Get sample metadata from SampleMetadata object |
| gini_index_per_sample | Gini index per sample |
| infile_column_index_options | Optparse options for infile column indices |
| infile_format_options | Optparse options for infile formatting |
| intermediate_qc_options | Optparse options for intermediate qc |
| library_annotation_column_index_options | Optparse options for library column indices |
| library_annotation_format_options | Optparse options for library formatting |
| library_annotation_genomic_column_index_options | Optparse options for library genomic column indices |
| library_annotation_options | Main optparse options for library annotations |
| LibraryAnnotations-class | An S4 class to represent library annotations |
| library_has_coordinates | Generic for library_has_coordinates method |
| library_has_coordinates-LibraryAnnotations-method | Check whether LibraryAnnotations object has coordinates |
| low_counts_per_sample | Low counts per sample |
| MageckGeneRRA-class | An S4 class to represent MAGeCK RRA gene summary |
| mageck_rra_summary_options | Optparse options for MAGeCK RRA gene summary |
| MageckSgrnaRRA-class | An S4 class to represent MAGeCK RRA sgRNA summary |
| plot_common_barplot | Generate bar plot |
| plot_common_density_ridges | Generate ridgeline density plot |
| plot_common_violin | Generate violin plot |
| plot_correlation | Generate correlation plot |
| plot_mageck_rra_gene_volcano | Plot MAGeCK RRA gene volcano |
| plot_mageck_rra_sgrna_barplot | Plot MAGeCK RRA sgRNA LFC barplot |
| plot_mapping_statistics | Plot read mapping statistics |
| plot_pca | Generate PCA plot. |
| plot_roc | Plot ROC |
| prepare_essentiality_data | Prepare BAGEL statistics |
| prepare_filepath | Prepare file path |
| prepare_pca | Prepare data for PCA plot |
| process_column_indices | Process column indices into vector. |
| process_roc | Process ROC |
| read_count_matrix_file | Read in sample count matrix. |
| read_file_to_dataframe | Read delimited file |
| read_fold_change_matrix_file | Read in sample fold change matrix. |
| read_library_annotation_file | Read library annotation file. |
| read_mageck_rra_gene_summary | Reads MAGeCK RRA gene summary |
| read_mageck_rra_sgrna_summary | Reads MAGeCK RRA sgRNA summary |
| read_sample_count_file | Read sample count file. |
| read_sample_count_files | Read sample count files. |
| read_sample_metadata_file | Read a sample metadata file. |
| remove_guide_options | Optparse options for output paths |
| remove_guides_from_count_matrix | Remove guides from count matrix. |
| remove_guides_from_library_annotations_object | Remove guides from library annotation object. |
| remove_guides_from_sample_counts | Remove guides from sample counts. |
| remove_no_coordinate_guide_options | Optparse options for removing guides with no coordinates |
| reorder_count_matrix_by_sample_type | Reorder count matrix by sample metadata. |
| SampleCounts-class | An S4 class to represent a single set of sample counts. |
| SampleMetadata-class | An S4 class to represent sample metadata (mapping) |
| sample_metadata_format_options | Optparse options for sample metadata formatting |
| sample_metadata_options | Main optparse options for sample metadata |
| sample_metadata_sample_filename_column_index_options | Optparse options for sample metadata count files column... |
| sample_metadata_sample_group_column_index_options | Optparse options for sample metadata sample group column... |
| sample_metadata_sample_label_column_index_options | Optparse options for sample metadata sample name column... |
| sample_metadata_sample_read_count_column_index_options | Optparse options for sample metadata read count column index |
| sample_metadata_sample_type_column_index_options | Optparse options for sample metadata sample type column... |
| save_plot_list | Save list of plots |
| save_plot_with_ggsave | Save plot with ggsave |
| scaling_options | Optparse options for scaling LFCs and BFs |
| sequencing_qc_options | Optparse options for raw count QC |
| shared_output_options | Optparse options for shared output |
| strip_id_options | Optparse options for stripping guide ids |
| total_counts_per_sample | Total counts per sample |
| write_dataframe_to_file | Write data frame to file. |
| write_rdata_to_file | Write R data to file. |
