# Precursor or Peptide Imputation under Random Truncation

## Documentation for package ‘Pirat’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

envPirat | Creates a BasiliskEnvironment class
estimate_gamma | Estimate missingness parameters Gamma
estimate_psi_df | Estimate psi and degrees of freedom
get_indexes_embedded_prots | Indexes of PGs embedded in each others
impute_block_llk_reset | Impute each PG.
impute_block_llk_reset_PG | Impute each PG.
impute_from_blocks | Impute abundance table from PGs results
my_pipeline_llkimpute | Pirat imputation function
pipeline_llkimpute | Pirat imputation function
pirat2SE | COnvert Pirat dataset to SummarizedExperiment
plot2hists | Plot 2 histograms
plot_pep_correlations | Empirical density of peptide correlations
rm_pg_from_idx_merge_pg | Remove PGs by index and merge
ropers | Ropers dataset
split_large_pg | Split too large PGs
split_large_pg_PG | Splits too large PGs in proteogenomics context
subbouyssie | Sub-Bouyssie dataset
subropers | Sub-Ropers dataset
wrapper_pipeline_llkimpute | Imputation method using SummarizedExperiment dataset