Package index • tso500R

Main Functions

Primary user-facing functions for creating data objects

cvo(): Read in a CombinedVariantOutput.tsv file and store as an object
cnv(): Read in a *CopyNumberVariants.vcf file and store as an object
qualitymetrics(): Read in a MetricsOutput.tsv file and store as an object
tmb(): Read in a TMB_trace.tsv file and store as an object

Reading Data Files

Import TSO500 data files

read_qmo_data(): Read in a batch of MetricsOutput.tsv files into a list
read_cvo_data(): Read in a batch of CombinedVariantOutput.tsv files into a list
read_small_variants(): Read in a list of combined.variant.output objects and return a data frame of small variants per sample
read_gene_amplifications(): Read in a list of combined.variant.output objects and return a data frame of gene amplifications per sample
read_fusions(): Read in a list of combined.variant.output objects and return a data frame of fusions per sample
read_splice_variants(): Read in a list of combined.variant.output objects and return a data frame of splice variants per sample
read_tmb_trace_data(): Read in a batch of TMB_trace.tsv files into a list
read_tmb_details_data(): Read in a batch of *tmb.json files into a list
read_tmb_details_data_csv(): Read in a batch of *tmb.metrics.csv files into a list
read_cnv_data(): Read in a batch of *CopyNumberVariants.vcf files into a list of CNV objects
read_annotation_data(): Read Excel spreadsheet into a list of data frames, per sheet
read_analysis_status(): Read in a list of combined.quality.metrics.output objects and return a data frame of the analysis status per timepoint
read_run_qc_metrics(): Read in a list of combined.quality.metrics.output objects and return a data frame of run qc metrics per timepoint

Quality Metrics

Extract and access QC metrics

get_analysis_details_df(): Extracts all analysis details from list of combined.variant.output objects, returning a data frame of analysis details per sample
get_analysis_status(): Extract the analysis status from combined.quality.metrics.output object and return in data frame format
get_analysis_status(<combined.quality.metrics.output>): Get analysis status from combined.quality.metrics.output object
get_count_df(): Extracts the counts of the different variant types from list of combined.variant.output objects, returning a data frame of counts per sample
get_dna_expanded_metrics(): Extract expanded dna qc metrics from combined.quality.metrics.output object and return in data frame format
get_dna_expanded_metrics(<combined.quality.metrics.output>): Get expanded dna qc metrics from combined.quality.metrics.output object
get_dna_qc_metrics(): Extract dna qc metrics from combined.quality.metrics.output object and return in data frame format
get_dna_qc_metrics(<combined.quality.metrics.output>): Get dna qc metrics from combined.quality.metrics.output object
get_dna_qc_metrics_cnv(): Extract dna qc metrics for CNV from combined.quality.metrics.output object and return in data frame format
get_dna_qc_metrics_cnv(<combined.quality.metrics.output>): Get dna qc metrics for cnv from combined.quality.metrics.output object
get_dna_qc_metrics_msi(): Extract dna qc metrics for msi from combined.quality.metrics.output object and return in data frame format
get_dna_qc_metrics_msi(<combined.quality.metrics.output>): Get dna qc metrics for msi from combined.quality.metrics.output object
get_dna_qc_metrics_snvtmb(): Extract dna qc metrics for small variants and tmb from combined.quality.metrics.output object and return in data frame format
get_dna_qc_metrics_snvtmb(<combined.quality.metrics.output>): Get dna qc metrics for small variants and tmb from combined.quality.metrics.output object
get_fusions(): Extract fusions from combined.variant.output object and return in data frame format
get_fusions(<combined.variant.output>): Get fusions from combined.variant.output object
get_gene_amplifications(): Extract gene amplifications from combined.variant.output object and return in data frame format
get_gene_amplifications(<combined.variant.output>): Get gene amplifications from combined.variant.output object
get_metrics_df(): Extracts all TMB/MSI metrics from list of combined.variant.output objects, returning a data frame of TMB/MSI per sample
get_rna_expanded_metrics(): Extract expanded rna qc metrics combined.quality.metrics.output object and return in data frame format
get_rna_expanded_metrics(<combined.quality.metrics.output>): Get expanded rna qc metrics from combined.quality.metrics.output object
get_rna_qc_metrics(): Extract rna qc metrics from combined.quality.metrics.output object and return in data frame format
get_rna_qc_metrics(<combined.quality.metrics.output>): Get rna qc metrics from combined.quality.metrics.output object
get_run_qc_metrics(): Extract run qc metrics from combined.quality.metrics.output object and return in data frame format
get_run_qc_metrics(<combined.quality.metrics.output>): Get run qc metrics from combined.quality.metrics.output object
get_sequencing_run_details_df(): Extracts all sequencing run details from list of combined.variant.output objects, returning a data frame of sequencing run details per sample
get_small_variants(): Extract small variants from combined.variant.output object and return in data frame format
get_small_variants(<combined.variant.output>): Get small variants from combined.variant.output object
get_splice_variants(): Extract splice variants from combined.variant.output object and return in data frame format
get_splice_variants(<combined.variant.output>): Get splice variants from combined.variant.output object
get_summarised_statistics_df(): Helper function to extract summarized counts based on sample_id
get_tmb_data(): Extract TMB data from tmb.variant.output object
get_tmb_data(<tmb.variant.output>): Extract TMB data from tmb.variant.output object
read_dna_expanded_metrics(): Read in a list of combined.quality.metrics.output objects and return a data frame of expanded dna qc metrics per timepoint
read_dna_qc_metrics(): Read in a list of combined.quality.metrics.output objects and return a data frame of dna qc metrics per timepoint
read_dna_qc_metrics_cnv(): Read in a list of combined.quality.metrics.output objects and return a data frame of dna qc metrics (cnv) per timepoint
read_dna_qc_metrics_msi(): Read in a list of combined.quality.metrics.output objects and return a data frame of dna qc metrics (msi) per timepoint
read_dna_qc_metrics_snvtmb(): Read in a list of combined.quality.metrics.output objects and return a data frame of dna qc metrics (small variants/tmb) per timepoint
read_rna_expanded_metrics(): Read in a list of combined.quality.metrics.output objects and return a data frame of expanded rna qc metrics per timepoint
read_rna_qc_metrics(): Read in a list of combined.quality.metrics.output objects and return a data frame of rna qc metrics per timepoint
extract_metrics(): Helper function to extract TMB/MSI metrics from list of combined.variant.output objects

Filtering and Processing

Filter and process variant data

process_and_filter_small_variant_data(): Process and filter small variant data-frame to requirements
filter_consequences(): Filters variant data for variant consequences. Removes any variant with a consequence matching the list of submitted consequences or an empty consequence field
filter_depth(): Helper function to filter small variant data according to specified depth
filter_for_cosmic_id(): Helper function to filter small variant data and keep only variants with annotated COSMIC ID(s)
filter_for_included_in_tmb(): Helper function to filter small variant data and keep only variants that are included in TMB numerator
filter_germline_db(): Helper function to filter small variant data according to the GermlineFilterDatabase filter
filter_germline_proxi(): Helper function to filter small variant data according to the GermlineFilterProxi filter
keep_consequences(): Filters for variant data for variant consequences. Keeps any variant with a consequence matching the list of submitted consequences

Data Integration

Combine and enrich data

add_tmb_variant_data(): Adds information from TMB trace table to small variant data
add_amplification_data(): Adds amplifications to small variant data, variant type (consequence_s) column renamed to variant_type
add_annotation_data(): Adds GEL annotation data to small variant data
get_metrics_df(): Extracts all TMB/MSI metrics from list of combined.variant.output objects, returning a data frame of TMB/MSI per sample
get_count_df(): Extracts the counts of the different variant types from list of combined.variant.output objects, returning a data frame of counts per sample
get_analysis_details_df(): Extracts all analysis details from list of combined.variant.output objects, returning a data frame of analysis details per sample
get_sequencing_run_details_df(): Extracts all sequencing run details from list of combined.variant.output objects, returning a data frame of sequencing run details per sample
summarize_cnv_data(): Read in a batch of *CopyNumberVariants.vcf files into one dataframe
update_annotation_join_columns(): Helper function to make small variant DF joinable to annotation data

Visualization

Create plots and tables

plot_af_density(): Plot allele-frequency kernel density estimate (KDE) for small variants
plot_af_histogram(): Plot allele-frequency histogram for small variants
plot_af_per_variant_consequence(): Plot allele-frequency for small variants per variant consequence
plot_onco_print(): Plot OncoPrint plot (heatmap) for variants
prepare_dataframe_for_oncoprint(): Transforms data frame holding variant information to a matrix that can be used as OncoPrint input
make_qc_table(): Visualize TSO500 QC results as gt-Table
add_common_theme_elements(): Add theme elements for visual customisation

Export and Writing

Export data and generate files

generate_dragen_samplesheet(): Generate sample sheet for DRAGEN TSO500 Anaylsis Pipeline input based on TSO500 sample sheet.
write_workbook(): Save data frames to Microsoft Excel workbook
write_worksheet(): Write worksheet to Excel workbook.
write_multiqc_data(): Write files needed for reporting in MultiQC.
write_rdata_file(): Save data frames to RData object.

Validation

Validate TSO500 data

validate_tso500(): Validator function for combined.variant.output constructor Not to be called directly NOT IMPLEMENTED
validate_tso500_qc(): Validator function for quality.metrics.output constructor Not to be called directly NOT IMPLEMENTED

Parsing Functions

Parse file formats and data structures

parse_illumina_samplesheet(): Parses DRAGEN sample sheet and returns a dataframe
parse_p_dot_notation(): Parses P-Dot notation column, splitting it into distinct NP ID and amino acid variant columns
parse_vcf_to_df(): Parse VCF files for a provided path and construct data frame.
parse_qmo_record(): Helper function to parse key-value lines in MetricsOutput.tsv
parse_qmo_table(): Helper function to parse tabular data in MetricsOutput.tsv
parse_cvo_record(): Helper function to parse key-value lines in CombinedVariantOutput.tsv
parse_cvo_table(): Helper function to parse tabular data in CombinedVariantOutput.tsv
handle_empty_qmo_table_values(): Helper function to handle empty rows in MetricsOutput.tsv tabular data
handle_empty_cvo_table_values(): Helper function to handle empty rows in CombinedVariantOutput.tsv tabular data
trim_qmo_header_and_footer(): Helper function to remove header and footer from MetricsOutput.tsv
trim_cvo_header_and_footer(): Helper function to remove header and footer from CombinedVariantOutput.tsv

Constructors

Internal constructor functions for data objects

new_combined_quality_metrics_output(): Constructor function for quality.metrics.output objects Not to be called directly
new_combined_variant_output(): Constructor function for combined.variant.output objects Not to be called directly
new_tmb_variant_output(): Constructor function for tmb.variant.output objects Not to be called directly
new_cnv_output(): Constructor function for combined.cnv.output objects Not to be called directly