
Package index
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import_mut_data()
- Import tabular mutation data
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import_vcf_data()
- Import a VCF file
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load_regions_file()
- Imports the regions file
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rename_columns()
- Map column names of mutation data to default column names. A utility function that renames columns of mutation data to default columns names.
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check_required_columns()
- Check that all required columns are present before proceeding with the function
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install_ref_genome()
- Install the reference genome for the specified organism.
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get_ref_of_mut()
- A utility function that will return the reference context of a mutation
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get_seq()
- Get sequence of genomic target regions
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get_cpg_regions()
- Get the coordinates of the CpG sites within your genomic regions
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annotate_cpg_sites()
- Annotate CpG sites
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context_list
- A list of reference contexts at different resolutions
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subtype_dict
- Values accepted for mutation subtypes
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subtype_list
- A list of mutation subtypes at different resolutions
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denominator_dict
- Values used for denominators in frequency calculations
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op
- Column names for mut tables
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reverseComplement()
- Get the reverse complement of a DNA or RNA sequence.
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classify_variation()
- classify_variation
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filter_mut()
- Filter your mutation data
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get_cpg_mutations()
- Get mutations at CpG sites.
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setup_mutseqr_python()
- Set up Python environment for MutSeqR
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calculate_mf()
- Calculate mutation frequency
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get_binom_ci()
- Add binomial confidence intervals to mutation frequencies.
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model_mf()
- Perform linear modelling on mutation frequency for given fixed and random effects
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sidak()
- Correct p-values for multiple comparisons
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plot_mf()
- Plot the Mutation Frequency
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plot_mean_mf()
- Plot the Mean Mutatation Frequency
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plot_model_mf()
- Plot your mf model
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plot_ci()
- plot_ci
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plot_spectra()
- Transition-transversion plot
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plot_trinucleotide()
- Plot the trinucleotide spectrum
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plot_trinucleotide_heatmap()
- Create a heatmap plot of mutation subtype proportions.
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spectra_comparison()
- Compare the overall mutation spectra between groups
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signature_fitting()
- Run COSMIC signatures comparison using SigProfilerAssignment
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cluster_spectra()
- Hierarchical Clustering
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plot_radar()
- Create a radar plot
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bmd_proast()
- BMD modeling using PROAST
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bmd_toxicr()
- BMD modeling using ToxicR
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f.proast()
- Run dose-response modeling using PROAST.
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f.plot.result()
- Plot the PROAST results
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f.plot.gui()
- Manages plotting for PROAST
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cleveland_plot()
- Cleveland Plot
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write_mutation_calling_file()
- Write the mutation calling file to input into the SigProfiler Assignment web application.
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write_mutational_matrix()
- Write a Mutational Matrix to input into the sigprofiler web application
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write_reference_fasta()
- Write FASTA file of reference sequences.
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write_vcf_from_mut()
- Write mutation_data to a VCF file
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write_excel()
- Write Excel tables
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render_report()
- Read configuration file and render R Markdown document
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plot_bubbles()
- Generate Bubble Plots
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plot_lollipop()
- Plot recurrent mutations in a lollipop plot using ggplot2
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print_ascii_art()
- This function prints ASCII art when the package is loaded