openSLD

openSLD parses Thermo Scientific Xcalibur sequence list (.sld) files into R data frames. It supports legacy and JSON-based layouts and extracts common sequence metadata together with optional user-defined fields.

Installation

Install the package from GitHub with:

# install.packages("pak")
# pak::pak("wilsontom/openSLD")
install.packages("openSLD", repos = c('https://wilsontom.r-universe.dev', 'https://cloud.r-project.org'))

Usage

library(openSLD)

path <- system.file(
  "extdata",
  "example-sequence.sld",
  package = "openSLD"
)

sequence <- parse_thermo_sld(path)
head(sequence)

The result contains one row per sequence entry. When present, the user-defined fields batch, block, class, injOrder, and sampleOrder are included. Missing user-defined fields are returned as NA.

Development

Run the test suite with:

testthat::test_local()

Require 100% test coverage with:

Rscript -e 'coverage <- covr::package_coverage(type = "tests"); print(coverage); stopifnot(covr::percent_coverage(coverage) == 100)'