Package: Pirat 0.99.26
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:
Pirat_0.99.26.tar.gz
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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
- ropers - Ropers dataset
- subbouyssie - Sub-Bouyssie dataset
- subropers - Sub-Ropers dataset
On BioConductor:Pirat-0.99.25(bioc 3.20)
Last updated 29 days agofrom:4a724fc806
Exports:envPiratestimate_gammaestimate_psi_dfget_indexes_embedded_protsimpute_block_llk_resetimpute_block_llk_reset_PGimpute_from_blocksinstall_Pirat_envmy_pipeline_llkimputepipeline_llkimputepirat2SEplot_pep_correlationsplot2histsrm_pg_from_idx_merge_pgsplit_large_pgsplit_large_pg_PGwrapper_pipeline_llkimpute
Dependencies:abindaskpassbasiliskbasilisk.utilsBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArraydir.expiryfansifarverfilelockGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtableherehmshttrinvgammaIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpngprettyunitsprogressR6rappdirsRColorBrewerRcppRcppTOMLreticulaterlangrprojrootS4ArraysS4VectorsscalesSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
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 |
| Install python environment for Pirat | install_Pirat_env |
| 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 |
