Function reference • miplicorn

Parse

These functions parse files obtained from MIPTools into tibbles.

read_tbl_reference() read_tbl_alternate() read_tbl_coverage() read_tbl_genotype() read_tbl_haplotype() read_tbl_ref_alt_cov(): Read MIPTools tables

label_mutations(): Label mutations

Manipulate

These functions are used to manipulate data objects.

filter_aa_change() filter_alt_umi_count() filter_coverage() filter_gene() filter_mutation_name() filter_ref_umi_count() filter_targeted(): Subset rows using a single column value

mutation_prevalence(): Compute prevalence of mutations

mutation_frequency(): Compute frequency of mutations

convert_single() convert_three(): Convert amino acid abbreviations

arrange_natural(): Arrange rows by column values naturally

Visualize

These functions are used to visualize data.

plot_chromoMap() plot_karyoploteR(): Create annotated chromosome map

plot_mutation_prevalence() autoplot(<mut_prev>) plot(<mut_prev>): Plot prevalence of mutations

plot_mutation_frequency() autoplot(<mut_freq>) plot(<mut_freq>): Plot frequency of mutations

theme_miplicorn() theme_rainbow(): Custom themes

Miscellaneous

These functions are used to inspect objects.

miplicorn_example(): Get path to miplicorn examples

Data

genome_Pf3D7: Plasmodium falciparum 3D7 genome