aggregate_metadata | Performs aggregation on metadata contained in the association file. |
aggregate_values_by_key | Aggregates matrices values based on specified key. |
annotation_issues | Check for genomic annotation problems in IS matrices. |
annotation_IS_vars | Current dynamic vars specifications getters. |
association_file | Example of association file. |
association_file_columns | Current dynamic vars specifications getters. |
as_sparse_matrix | Converts tidy integration matrices in the original sparse matrix form. |
available_outlier_tests | A character vector containing all the names of the currently supported outliers tests that can be called in the function outlier_filter. |
available_tags | All available tags for dynamic vars look-up tables. |
blood_lineages_default | Default blood lineages info |
circos_genomic_density | Trace a circos plot of genomic densities. |
CIS_grubbs | Grubbs test for Common Insertion Sites (CIS). |
CIS_grubbs_overtime | Compute CIS and Grubbs test over different time points and groups. |
CIS_volcano_plot | Trace volcano plot for computed CIS data. |
clinical_relevant_suspicious_genes | Clinical relevant suspicious genes (for mouse and human). |
comparison_matrix | Obtain a single integration matrix from individual quantification matrices. |
compute_abundance | Computes the abundance for every integration event in the input data frame. |
compute_near_integrations | Scans input matrix to find and merge near integration sites. |
cumulative_is | Expands integration matrix with the cumulative IS union over time. |
date_formats | Possible choices for the 'dates_format' parameter in 'import_association_file', 'import_parallel_vispa2Matrices_interactive' and 'import_parallel_vispa2Matrices_auto'. |
default_af_transform | Default transformations to apply to association file columns. |
default_iss_file_prefixes | Default regex prefixes for Vispa2 stats files. |
default_meta_agg | Default metadata aggregation function table |
default_rec_agg_lambdas | Defaults for column aggregations in 'compute_near_integrations()'. |
default_report_path | Default folder for saving ISAnalytics reports. Supplied as default argument for several functions. |
default_stats | A set of pre-defined functions for 'sample_statistics'. |
enable_progress_bars | Enable global progress bars for ISAnalytics functions. |
export_ISA_settings | Export a dynamic vars settings profile. |
fisher_scatterplot | Plot results of gene frequency Fisher's exact test. |
generate_blank_association_file | Create a blank association file. |
generate_default_folder_structure | Generate a default folder structure, following VISPA2 standards |
generate_Vispa2_launch_AF | Creates a reduced association file for a VISPA2 run, given project and pool |
gene_frequency_fisher | Compute Fisher's exact test on gene frequencies. |
HSC_population_plot | Plot of the estimated HSC population size for each patient. |
HSC_population_size_estimate | Hematopoietic stem cells population size estimate. |
import_association_file | Import the association file from disk |
import_ISA_settings | Import a dynamic vars settings profile. |
import_parallel_Vispa2Matrices | Import integration matrices from paths in the association file. |
import_single_Vispa2Matrix | Import a single integration matrix from file |
import_Vispa2_stats | Import Vispa2 stats given the aligned association file. |
inspect_tags | Retrieve description of a tag by name. |
integration_alluvial_plot | Alluvial plots for IS distribution in time. |
integration_matrices | Example of imported multi-quantification integration matrices. |
iss_source | Find the source of IS by evaluating sharing. |
iss_stats_specs | Current dynamic vars specifications getters. |
is_sharing | Sharing of integration sites between given groups. |
known_clinical_oncogenes | Known clinical oncogenes (for mouse and human). |
mandatory_IS_vars | Current dynamic vars specifications getters. |
matching_options | Possible choices for the 'matching_opt' parameter. |
matrix_file_suffixes | Current dynamic vars specifications getters. |
NGSdataExplorer | Launch the shiny application NGSdataExplorer. |
outliers_by_pool_fragments | Identify and flag outliers based on pool fragments. |
outlier_filter | Filter out outliers in metadata, identified by the chosen outlier test. |
pcr_id_column | Easily retrieve the name of the pcr id column. |
proto_oncogenes | Data frames for proto-oncogenes (human and mouse) amd tumor-suppressor genes from UniProt. |
purity_filter | Filter integration sites based on purity. |
quantification_types | Possible choices for the 'quantification_type' parameter. |
realign_after_collisions | Re-aligns matrices of other quantification types based on the processed sequence count matrix. |
reduced_AF_columns | Names of the columns of the association file to consider for Vispa2 launch. |
refGenes_hg19 | Gene annotation files for hg19, mm9 and mm10. |
refGenes_mm9 | Gene annotation files for hg19, mm9 and mm10. |
refGene_table_cols | Required columns for refGene file. |
remove_collisions | Identifies and removes collisions. |
reset_af_columns_def | Resets dynamic vars to the default values. |
reset_annotation_IS_vars | Resets dynamic vars to the default values. |
reset_dyn_vars_config | Resets dynamic vars to the default values. |
reset_iss_stats_specs | Resets dynamic vars to the default values. |
reset_mandatory_IS_vars | Resets dynamic vars to the default values. |
reset_matrix_file_suffixes | Resets dynamic vars to the default values. |
sample_statistics | Computes user specified functions on numerical columns and updates the metadata data frame accordingly. |
separate_quant_matrices | Separate a multiple-quantification matrix into single quantification matrices. |
set_af_columns_def | Define custom dynamic vars. |
set_annotation_IS_vars | Define custom dynamic vars. |
set_iss_stats_specs | Define custom dynamic vars. |
set_mandatory_IS_vars | Define custom dynamic vars. |
set_matrix_file_suffixes | Sets the look-up table for matrix file suffixes. |
sharing_heatmap | Plot IS sharing heatmaps. |
sharing_venn | Produce tables to plot sharing venn or euler diagrams. |
threshold_filter | Filter data frames with custom predicates |
top_abund_tableGrob | Summary top abundant tableGrobs for plots. |
top_cis_overtime_heatmap | Heatmaps for the top N common insertion sites over time. |
top_integrations | Sorts and keeps the top n integration sites based on the values in a given column. |
top_targeted_genes | Top n targeted genes based on number of IS. |
transform_columns | Apply transformations to an arbitrary number of columns. |
tumor_suppressors | Data frames for proto-oncogenes (human and mouse) amd tumor-suppressor genes from UniProt. |
vars_getters | Current dynamic vars specifications getters. |
vars_resetters | Resets dynamic vars to the default values. |
vars_setters | Define custom dynamic vars. |