# Pirat
## Installation
To install this package from Github:
```
install.packages('remotes')
remotes::install_github('prostarproteomics/Pirat')
```
Once the package has been downloaded, it is necessary to install a Python
environment with specific versions of Python libraries. This is the purpose of
the function `install_Pirat_env()`. This function takes a long time to execute
and need to be run only once.
```
library(Pirat)
install_Pirat_env()
```
## Test
```
data(subbouyssie)
my_pipeline_llkimpute(subbouyssie)
data(subropers)
nsamples = nrow(subropers$peptides_ab)
my_pipeline_llkimpute(subropers,
extension = "T",
rna.cond.mask = 1:nsamples,
pep.cond.mask = 1:nsamples,
max.pg.size.pirat.t = 1)
```
