Package: Pirat 1.1.0

Samuel Wieczorek

Pirat: Precursor or Peptide Imputation under Random Truncation

Pirat enables the imputation of missing values (either MNARs or MCARs) in bottom-up LC-MS/MS proteomics data using a penalized maximum likelihood strategy. It does not require any parameter tuning, it models the instrument censorship from the data available. It accounts for sibling peptides correlations and it can leverage complementary transcriptomics measurements.

Authors:Lucas Etourneau [aut], Laura Fancello [aut], Samuel Wieczorek [cre, aut], Nelle Varoquaux [aut], Thomas Burger [aut]

Pirat_1.1.0.tar.gz
Pirat_1.1.0.zip(r-4.5)Pirat_1.1.0.zip(r-4.4)
Pirat_1.1.0.tgz(r-4.5-any)Pirat_1.1.0.tgz(r-4.4-any)
Pirat_1.1.0.tar.gz(r-4.5-noble)Pirat_1.1.0.tar.gz(r-4.4-noble)
Pirat_1.1.0.tgz(r-4.4-emscripten)
Pirat.pdf |Pirat.html✨
Pirat/json (API)
NEWS

# Install 'Pirat' in R:

install.packages('Pirat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/prostarproteomics/pirat/issues

Datasets:

ropers - Ropers dataset
subbouyssie - Sub-Bouyssie dataset
subropers - Sub-Ropers dataset

On BioConductor:Pirat-1.1.0(bioc 3.21)Pirat-1.0.2(bioc 3.20)

proteomics massspectrometry preprocessing software

4.78 score 9 scripts 125 downloads 16 exports 68 dependencies

Last updated 5 months agofrom:d00d34343f. Checks:1 OK, 1 ERROR, 5 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 18 2025
R-4.5-win	NOTE	Mar 18 2025
R-4.5-mac	NOTE	Mar 18 2025
R-4.5-linux	ERROR	Mar 18 2025
R-4.4-win	NOTE	Mar 18 2025
R-4.4-mac	NOTE	Mar 18 2025
R-4.4-linux	NOTE	Mar 18 2025

Exports:envPirat estimate_gamma estimate_psi_df get_indexes_embedded_prots impute_block_llk_reset impute_block_llk_reset_PG impute_from_blocks my_pipeline_llkimpute pipeline_llkimpute pirat2SE plot_pep_correlations plot2hists rm_pg_from_idx_merge_pg split_large_pg split_large_pg_PG wrapper_pipeline_llkimpute

Dependencies:abind askpass basilisk basilisk.utils Biobase BiocGenerics cli colorspace crayon curl DelayedArray dir.expiry fansi farver filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gtable here hms httr invgamma IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig png prettyunits progress R6 rappdirs RColorBrewer Rcpp RcppTOML reticulate rlang rprojroot S4Arrays S4Vectors scales SparseArray SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector

Pirat

Lucas Etourneau, Samuel Wieczorek"

Rendered fromPirat.Rmdusingknitr::rmarkdownon Mar 18 2025.

Last update: 2024-09-18
Started: 2024-03-13

Citation

Development and contributors

Readme and manuals

Help Manual

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