Analysis of Error-Corrected Sequencing Data for Mutation Detection

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Documentation for package ‘MutSeqR’ version 0.99.9

• DESCRIPTION file
• 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
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
import_mut_data	Import tabular mutation data
import_regions_metadata	Join Regions Metadata
import_sample_data	Join 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
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.
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
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