# Analysis of Error-Corrected Sequencing Data for Mutation Detection

## Documentation for package ‘MutSeqR’ version 1.0.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

annotate_cpg_sites | Annotate CpG sites
bmd_proast | BMD modeling using PROAST
BS_org_map | BS genome organism dictionary
calculate_mf | Calculate mutation frequency
characterize_variants | Characterize Variants
check_required_columns | Check that all required columns are present before proceeding with the function
classify_variation | classify_variation
cleveland_plot | Cleveland Plot
cluster_spectra | Hierarchical Clustering
context_list | A list of reference contexts at different resolutions
denominator_dict | Values used for denominators in frequency calculations
dm_loglik_ridge_stable | dm_loglik_ridge_stable
f.plot.gui | Manages plotting for PROAST
f.plot.result | Plot the PROAST results
f.proast | Run dose-response modeling using PROAST.
filter_mut | Filter your mutation data
find_BS_genome | Find the appropriate BS genome for the specified organism and genome.
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_ref_of_mut | A utility function that will return the reference context of a mutation
get_seq | Get sequence of genomic target regions
get_vcf_end_positions | Derive end coordinates from a VCF object
import_mut_data | Import tabular mutation data
import_regions_metadata | Join Regions Metadata
import_sample_data | Import Sample Metadata
import_vcf_data | Import a VCF file
load_regions_file | Imports the regions file
model_mf | Perform linear modelling on mutation frequency for given fixed and random effects
op | Dictionary of column name synonyms for required mutation data columns
plot_bubbles | Generate Bubble Plots
plot_ci | plot_ci
plot_lollipop | Plot recurrent mutations in a lollipop plot using ggplot2
plot_mean_mf | Plot the Mean Mutatation Frequency
plot_mf | Plot the Mutation Frequency
plot_model_mf | Plot your mf model
plot_radar | Create a radar plot
plot_spectra | Plot spectra
plot_trinucleotide | Plot the trinucleotide spectrum
plot_trinucleotide_heatmap | Create a heatmap plot of mutation subtype proportions.
populate_sequence_context | Populate Sequence context
print_ascii_art | This function prints ASCII art when the package is loaded
rdm_fast | rdm_fast
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.
render_report | Read configuration file and render R Markdown document
reverseComplement | Get the reverse complement of a DNA or RNA sequence.
run_penalized_comparison | run_penalized_comparison
select_optimal_lambda | select_optimal_lambda
setup_mutseqr_python | Set up Python environment for MutSeqR
sidak | Correct p-values for multiple comparisons
signature_fitting | Run COSMIC signatures comparison using SigProfilerAssignment
spectra_comparison | Compare the overall mutation spectra between groups
spectra_comparison_rpdmm | spectra_comparison_rpdmm
subtype_dict | Subtype Resolution Dictionary
subtype_list | A comprehensive list of mutation subtypes at different resolutions
vcf_sample_fix | Retrieve the sample column from VCF files
write_excel | Write results to Excel tables
write_mutational_matrix | Write a Mutational Matrix to input into the sigprofiler web application
write_mutation_calling_file | Write the mutation calling file to input into the SigProfiler Assignment web application.
write_reference_fasta | Write FASTA file of reference sequences.
write_vcf_from_mut | Write mutation_data to a VCF file