readthis

The goal of readthis is to provide functions for convenient reading outputs from programs and algorithms such as CliP, Strelka ect.

Installation

You can install the development version of readthis from GitHub with:

devtools::install_github("pawelqs/readthis")

Currently supported algorithms and tools

Variant Callers:

• Strelka2 (somatic SNVs only): read_strelka_somatic_snvs()
• Mutect2 SNVs: read_mutect_snvs()
• FACETS CNAs: read_facets_cnas()
• ASCAT CNAs: read_ascat_files() (does not work with all the files)

Other tools:

• CliP is an algorithm for clonal structure identification through penalizing pairwise differences:
  • read_clip_all()
  • read_clip_all_wide()
  • read_clip_best_lambda()

Interface

In most functions, the first argument can be either:

• path to a single file
• vector of file paths, element names will be used as patient IDs/sample IDs
• path to a directory containing multiple files, patient/sample IDs will be guessed from the file names.

See the function’s help pages (e.g. ?read_strelka_somatic_snvs) for more details.

Example

library(readthis)
dir <- system.file("CliP", package = "readthis")
read_clip_best_lambda(dir)