Installation | Standard imputation with Pirat | Intra-PG correlation analysis | Pirat extensions | -2, the 2-peptide rule | -S, samples-wise correlations | -T, transcriptomic integration | 5. Session info | References
Package: Pirat 1.7.0
Lucas Etourneau
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:
Pirat_1.7.0.tar.gz
Pirat_1.7.0.zip(r-4.7)Pirat_1.7.0.zip(r-4.6)Pirat_1.7.0.zip(r-4.5)
Pirat_1.7.0.tgz(r-4.6-any)Pirat_1.7.0.tgz(r-4.5-any)
Pirat_1.7.0.tar.gz(r-4.7-any)Pirat_1.7.0.tar.gz(r-4.6-any)
Pirat_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Pirat/json (API)
| # Install 'Pirat' in R: |
| install.packages('Pirat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/edyp-lab/pirat/issues
Datasets:
- ropers - Ropers dataset
- subbouyssie - Sub-Bouyssie dataset
- subropers - Sub-Ropers dataset
On BioConductor:Pirat-1.7.0(bioc 3.24)Pirat-1.6.0(bioc 3.23)
proteomicsmassspectrometrypreprocessingsoftwareprostar2
Last updated from:61147561f4. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 174 | ||
| linux-devel-x86_64 | NOTE | 917 | ||
| source / vignettes | OK | 868 | ||
| linux-release-x86_64 | NOTE | 869 | ||
| macos-release-arm64 | NOTE | 490 | ||
| macos-oldrel-arm64 | NOTE | 645 | ||
| windows-devel | NOTE | 359 | ||
| windows-release | NOTE | 377 | ||
| windows-oldrel | NOTE | 341 | ||
| wasm-release | OK | 167 |
Exports:envPiratestimate_gammaestimate_psi_dfget_indexes_embedded_protsimpute_block_llk_resetimpute_block_llk_reset_PGimpute_from_blocksmy_pipeline_llkimputepipeline_llkimputepirat2SEplot_pep_correlationsplot2histsrm_pg_from_idx_merge_pgsplit_large_pgsplit_large_pg_PGwrapper_pipeline_llkimpute
Dependencies:abindbasiliskBiobaseBiocGenericsclicpp11crayonDelayedArraydir.expiryfarverfilelockgenericsGenomicRangesggplot2gluegtableherehmsinvgammaIRangesisobandjsonlitelabelinglatticelifecycleMASSMatrixMatrixGenericsmatrixStatspkgconfigpngprettyunitsprogressR6rappdirsRColorBrewerRcppRcppTOMLreticulaterlangrprojrootS4ArraysS4VectorsS7scalesSeqinfoSparseArraySummarizedExperimentvctrsviridisLitewithrXVector
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 |
