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

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Documentation for package ‘ISAnalytics’ version 1.19.3

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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.