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 CNVs:
read_facets_cnvs()
- ASCAT CNVs:
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)