Package index • MutSeqR

General Usage

Functions for importing, filtering, and summarizing mutation data.

import_mut_data(): Import tabular mutation data
import_vcf_data(): Import a VCF file
filter_mut(): Filter your mutation data
calculate_mf(): Calculate mutation frequency
load_regions_file(): Imports the regions file
find_BS_genome(): Find the appropriate BS genome for the specified organism and genome.
classify_variation(): classify_variation

Functions to model and visualize mutation frequency.

plot_mf(): Plot the Mutation Frequency
plot_mean_mf(): Plot the Mean Mutatation Frequency
model_mf(): Perform linear modelling on mutation frequency for given fixed and random effects
plot_model_mf(): Plot your mf model
sidak(): Correct p-values for multiple comparisons
bmd_proast(): BMD modeling using PROAST
plot_ci(): plot_ci

Analysis and visualization of mutation spectra.

plot_spectra(): Plot spectra
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

General plotting functions.

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

Predefined dictionaries and utility functions.

BS_org_map: BS genome organism dictionary
context_list: A list of reference contexts at different resolutions
subtype_dict: Subtype Resolution Dictionary
subtype_list: A comprehensive list of mutation subtypes at different resolutions
denominator_dict: Values used for denominators in frequency calculations
op: Dictionary of column name synonyms for required mutation data columns

Data 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

annotate_cpg_sites(): Annotate CpG sites
get_binom_ci(): Add binomial confidence intervals to mutation frequencies.
get_cpg_mutations(): Get mutations at CpG sites.
get_cpg_regions(): Get the coordinates of the CpG sites within your genomic regions
get_seq(): Get sequence of genomic target regions

print_ascii_art(): This function prints ASCII art when the package is loaded
import_regions_metadata(): Join Regions Metadata
import_sample_data(): Join Sample Metadata
populate_sequence_context(): Populate Sequence context
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
get_ref_of_mut(): A utility function that will return the reference context of a mutation
reverseComplement(): Get the reverse complement of a DNA or RNA sequence.
characterize_variants(): Characterize Variants
setup_mutseqr_python(): Set up Python environment for MutSeqR
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