Package index • MutSeqR

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