Package index • ISAnalytics

Import functions

Importing integration matrices and metadata from files

import_association_file() stable: Import the association file from disk

import_Vispa2_stats() stable: Import Vispa2 stats given the aligned association file.

import_single_Vispa2Matrix() stable: Import a single integration matrix from file

import_parallel_Vispa2Matrices() stable: Import integration matrices from paths in the association file.

Data cleaning and pre-processing

annotation_issues() experimental: Check for genomic annotation problems in IS matrices.

compute_near_integrations() stable: Scans input matrix to find and merge near integration sites.

remove_collisions() stable: Identifies and removes collisions.

realign_after_collisions() stable: Re-aligns matrices of other quantification types based on the processed sequence count matrix.

outlier_filter() experimental: Filter out outliers in metadata, identified by the chosen outlier test.

outliers_by_pool_fragments() stable: Identify and flag outliers based on pool fragments.

aggregate_metadata() stable: Performs aggregation on metadata contained in the association file.

aggregate_values_by_key() stable: Aggregates matrices values based on specified key.

Analysis functions

compute_abundance() stable: Computes the abundance for every integration event in the input data frame.

top_integrations() stable: Sorts and keeps the top n integration sites based on the values in a given column.

top_targeted_genes() experimental: Top n targeted genes based on number of IS.

sample_statistics() stable: Computes user specified functions on numerical columns and updates the metadata data frame accordingly.

CIS_grubbs() stable: Grubbs test for Common Insertion Sites (CIS).

CIS_grubbs_overtime() experimental: Compute CIS and Grubbs test over different time points and groups.

gene_frequency_fisher() experimental: Compute Fisher's exact test on gene frequencies.

cumulative_is() experimental: Expands integration matrix with the cumulative IS union over time.

is_sharing() stable: Sharing of integration sites between given groups.

purity_filter() stable: Filter integration sites based on purity.

iss_source() stable: Find the source of IS by evaluating sharing.

HSC_population_size_estimate() stable: Hematopoietic stem cells population size estimate.

Plotting functions

CIS_volcano_plot() stable: Trace volcano plot for computed CIS data.

top_cis_overtime_heatmap() experimental: Heatmaps for the top N common insertion sites over time.

HSC_population_plot(): Plot of the estimated HSC population size for each patient.

integration_alluvial_plot() stable: Alluvial plots for IS distribution in time.

top_abund_tableGrob(): Summary top abundant tableGrobs for plots.

sharing_heatmap() stable: Plot IS sharing heatmaps.

sharing_venn() stable: Produce tables to plot sharing venn or euler diagrams.

circos_genomic_density() stable: Trace a circos plot of genomic densities.

fisher_scatterplot() stable: Plot results of gene frequency Fisher's exact test.

Utility functions

as_sparse_matrix() stable: Converts tidy integration matrices in the original sparse matrix form.

generate_blank_association_file(): Create a blank association file.

generate_Vispa2_launch_AF(): Creates a reduced association file for a VISPA2 run, given project and pool

inspect_tags(): Retrieve description of a tag by name.

available_tags(): All available tags for dynamic vars look-up tables.

set_mandatory_IS_vars() set_annotation_IS_vars() set_af_columns_def() set_iss_stats_specs(): Define custom dynamic vars.

reset_mandatory_IS_vars() reset_annotation_IS_vars() reset_af_columns_def() reset_iss_stats_specs() reset_matrix_file_suffixes() reset_dyn_vars_config(): Resets dynamic vars to the default values.

mandatory_IS_vars() annotation_IS_vars() association_file_columns() iss_stats_specs() matrix_file_suffixes(): Current dynamic vars specifications getters.

set_matrix_file_suffixes(): Sets the look-up table for matrix file suffixes.

export_ISA_settings(): Export a dynamic vars settings profile.

import_ISA_settings(): Import a dynamic vars settings profile.

pcr_id_column(): Easily retrieve the name of the pcr id column.

transform_columns(): Apply transformations to an arbitrary number of columns.

comparison_matrix() stable: Obtain a single integration matrix from individual quantification matrices.

separate_quant_matrices() stable: Separate a multiple-quantification matrix into single quantification matrices.

generate_default_folder_structure(): Generate a default folder structure, following VISPA2 standards

enable_progress_bars(): Enable global progress bars for ISAnalytics functions.

NGSdataExplorer(): Launch the shiny application NGSdataExplorer.

Exported variables and helpers

date_formats(): Possible choices for the dates_format parameter in import_association_file, import_parallel_vispa2Matrices_interactive and import_parallel_vispa2Matrices_auto.

matching_options(): Possible choices for the matching_opt parameter.

quantification_types(): Possible choices for the quantification_type parameter.

reduced_AF_columns(): Names of the columns of the association file to consider for Vispa2 launch.

default_stats(): A set of pre-defined functions for sample_statistics.

clinical_relevant_suspicious_genes(): Clinical relevant suspicious genes (for mouse and human).

known_clinical_oncogenes(): Known clinical oncogenes (for mouse and human).

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.

blood_lineages_default(): Default blood lineages info

default_iss_file_prefixes(): Default regex prefixes for Vispa2 stats files.

default_meta_agg(): Default metadata aggregation function table

default_report_path(): Default folder for saving ISAnalytics reports. Supplied as default argument for several functions.

refGene_table_cols(): Required columns for refGene file.

default_af_transform(): Default transformations to apply to association file columns.

default_rec_agg_lambdas(): Defaults for column aggregations in compute_near_integrations().

Deprecated

import_parallel_Vispa2Matrices_interactive() defunct: Import integration matrices from association file.

import_parallel_Vispa2Matrices_auto() defunct: Import integration matrices from association file.

cumulative_count_union() defunct: Integrations cumulative count in time by sample

unzip_file_system() deprecated: A utility function to unzip and use example file systems included in the package

threshold_filter() deprecated: Filter data frames with custom predicates

Data

association_file: Example of association file.

integration_matrices: Example of imported multi-quantification integration matrices.

proto_oncogenes tumor_suppressors: Data frames for proto-oncogenes (human and mouse) and tumor-suppressor genes from UniProt.

refGenes_hg19 refGenes_mm9: Gene annotation files for hg19, mm9.

refGenes_hg38 refGenes_mm10: Reference gene annotation for hg38 or mm10.