NEWS.md

In bailey-lab/miplicorn: A Framework for Molecular Inversion Probe and Amplicon Analysis

miplicorn (development version)

• Improve documentation by adding return values, rewriting examples, and updating the README.
• New plot_coverage() function can be used to plot the average coverage across a given grouping variable (#46).
• The column created by label_mutations() has been renamed from ans_der_indel to mutation_label (#44).
• label_mutations() more clearly signals when the computation can not be completed. This can occur because of missing variables or an incorrect input table (#44).
• Improve condition signalling by using {cli}. Messages are now properly pluralized and display the erroring function (#42).
• Improve performance of amino acid conversion functions (#40).
• Define classes for all input tables. These classes allow developers to control which inputs work with which functions (#38, #39).
• Add the capability to compute the prevalence of mutations using genotype tables instead of the combined reference, alternate, and coverage table (#37).
• Set minimum {dplyr} version to 1.0.0.
• Add an internal check on the version of {chromoMap}.
• Replace NA or NaN results with zero when computing the prevalence of mutations.

miplicorn 0.2.1

• We now account for the UMI threshold when computing the frequency of mutations (#35).
• New read_tbl_genotype() function can be used to read in the genotypes_AA_table.csv and genotypes_AN_table.csv generated by MIPTools (#34).

miplicorn 0.2.0

Breaking changes

• Minimum R version has been bumped up to 3.4. This reflects the minimum version defined by package imports.
• Deprecate chromosome_map() in favor of plot_chromoMap() and plot_karyoploteR() (#25).

Read files

• The new read_tbl_*() family of functions provides a consistent function call to read data tables generated by MIPTools (#17).
• read_tbl_haplotype() can be used to read the haplotypes_count.csv file generated by MIPTools (#15).

New features

• New vignette("faq") answers some frequently asked questions (#32).
• New mutation_frequency() and plot_mutation_frequency() functions can be used to determine the frequency of mutations (#29).
• New mutation_prevalence() and plot_mutation_prevalence() functions can be used to determine the prevalence of mutations (#23).
• New label_mutations() labels a mutation as "ref", "alt", "ins", or "del" (#3).
• New theme_rainbow() creates a custom theme.

Minor improvements and bug fixes

• plot_karyoploteR() no longer prints plot noisily.
• read_tbl_*() functions no longer change sample IDs (#20).
• We now use {rlang} instead of {cli} to display messages, warnings, and errors (#16).
• plot_karyoploteR() now works for arbitrary column names (#14).

miplicorn 0.1.0

• chromosome_map() can now create an additional type of map (#11).
• New chromosome_map() creates a chromosome map annotated with probe locations.
• theme_miplicorn() specifies a custom theme for creating figures.
• read() now allows for filtering on multiple conditions (#7).
• New arrange_natural() naturally sorts a data frame (#5).
• New convert_single() and convert_three convert amino acid abbreviations (#1).
• Increase efficiency of read() (#2).
• Added a NEWS.md file to track changes to the package.

bailey-lab/miplicorn documentation built on March 19, 2023, 7:40 p.m.