Precursor or Peptide Imputation under Random Truncation

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Documentation for package ‘Pirat’ version 1.2.2

• 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