Rdirectlfq is an R package that runs the directlfq Python library to calculate protein abundance using ion abundance.

You can install the development version of Rdirectlfq like so:

devtools::install_github("mildpiggy/directlfq")

The packages require a python conda environment with dircetlfq library. Your can check and deploy this conda environment by check_directlfq_Module

check_directlfq_Module(confirm_or_not = T)

This is a basic example which shows you how to solve a common problem:

library(Rdirectlfq)
data(example_diann_res) ## A diann result from report.tsv
pro_int = directlfq(example_diann_res,reformatted = F)

## A generic input table, which has been reformatted.
data(example_generic_input)
pro_int = directlfq(example_generic_input, reformatted = T)

For more detailed information on the input table, please refer to the GitHub repository of MannLabs: https://github.com/MannLabs/directlfq.

Any issues encountered during the use can be submitted through the issue tracker or by contacting the developer.