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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
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options(tibble.print_min = 5, tibble.print_max = 5)

miplicorn

miplicorn establishes a unified analysis framework in R for molecular inversion probe (MIP) and amplicon-targeted sequencing analysis after micro haplotyping or variant calling. It provides tools for parsing large variant files, filtering and manipulating the data, and basic analyses and visualization.

Installation

You may install the package from Github using devtools.

::: .pkgdown-release

# Install most recent released version
devtools::install_github("bailey-lab/miplicorn@v0.2.1")

:::

::: .pkgdown-devel

# Install development version
devtools::install_github("bailey-lab/miplicorn")

:::

Usage

See vignette("miplicorn") for a more extensive introduction and a demonstration of several features of the package.

library(miplicorn)

ref_file <- miplicorn_example("reference_AA_table.csv")
alt_file <- miplicorn_example("alternate_AA_table.csv")
cov_file <- miplicorn_example("coverage_AA_table.csv")

data <- read_tbl_ref_alt_cov(ref_file, alt_file, cov_file, gene == "atp6" | gene == "crt")
data

plot_coverage(data, mutation_name)

prev <- mutation_prevalence(data, threshold = 5)
prev

plot(prev)

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