# Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

## Documentation for package ‘ISAnalytics’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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) and 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.
refGenes_hg38 | Reference gene annotation for hg38 or mm10.
refGenes_mm10 | Reference gene annotation for hg38 or mm10.
refGenes_mm9 | Gene annotation files for hg19, mm9.
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.
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) and 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.