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Data Import

Functions for importing and preparing mutation and region data.

import_mut_data()
Import tabular mutation data
import_vcf_data()
Import a VCF file
load_regions_file()
Imports the regions file
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.
check_required_columns()
Check that all required columns are present before proceeding with the function

Reference Genomes & Context

Reference sequence utilities.

install_ref_genome()
Install the reference genome for the specified organism.
get_ref_of_mut()
A utility function that will return the reference context of a mutation
get_seq()
Get sequence of genomic target regions
get_cpg_regions()
Get the coordinates of the CpG sites within your genomic regions
annotate_cpg_sites()
Annotate CpG sites
context_list
A list of reference contexts at different resolutions
subtype_dict
Values accepted for mutation subtypes
subtype_list
A list of mutation subtypes at different resolutions
denominator_dict
Values used for denominators in frequency calculations
op
Column names for mut tables
reverseComplement()
Get the reverse complement of a DNA or RNA sequence.

Mutation Data Handling

Wrangling and filtering mutation tables.

classify_variation()
classify_variation
filter_mut()
Filter your mutation data
get_cpg_mutations()
Get mutations at CpG sites.
setup_mutseqr_python()
Set up Python environment for MutSeqR

Mutation Frequency Analysis

Functions to calculate, model, and visualize mutation frequency.

calculate_mf()
Calculate mutation frequency
get_binom_ci()
Add binomial confidence intervals to mutation frequencies.
model_mf()
Perform linear modelling on mutation frequency for given fixed and random effects
sidak()
Correct p-values for multiple comparisons
plot_mf()
Plot the Mutation Frequency
plot_mean_mf()
Plot the Mean Mutatation Frequency
plot_model_mf()
Plot your mf model
plot_ci()
plot_ci

Spectra and Subtypes

Analysis and visualization of mutation spectra.

plot_spectra()
Transition-transversion plot
plot_trinucleotide()
Plot the trinucleotide spectrum
plot_trinucleotide_heatmap()
Create a heatmap plot of mutation subtype proportions.
spectra_comparison()
Compare the overall mutation spectra between groups
signature_fitting()
Run COSMIC signatures comparison using SigProfilerAssignment
cluster_spectra()
Hierarchical Clustering
plot_radar()
Create a radar plot

Dose-Response / BMD Modeling

Functions for BMD modeling using PROAST and ToxicR.

bmd_proast()
BMD modeling using PROAST
bmd_toxicr()
BMD modeling using ToxicR
f.proast()
Run dose-response modeling using PROAST.
f.plot.result()
Plot the PROAST results
f.plot.gui()
Manages plotting for PROAST
cleveland_plot()
Cleveland Plot

Mutation Output

Export functions.

write_mutation_calling_file()
Write the mutation calling file to input into the SigProfiler Assignment web application.
write_mutational_matrix()
Write a Mutational Matrix to input into the sigprofiler web application
write_reference_fasta()
Write FASTA file of reference sequences.
write_vcf_from_mut()
Write mutation_data to a VCF file
write_excel()
Write Excel tables
render_report()
Read configuration file and render R Markdown document

Visualization Utilities

plot_bubbles()
Generate Bubble Plots
plot_lollipop()
Plot recurrent mutations in a lollipop plot using ggplot2

Internal or Miscellaneous

print_ascii_art()
This function prints ASCII art when the package is loaded