Package: PolySTest 1.1.0

Veit Schwämmle

PolySTest: PolySTest: Detection of differentially regulated features. Combined statistical testing for data with few replicates and missing values

The complexity of high-throughput quantitative omics experiments often leads to low replicates numbers and many missing values. We implemented a new test to simultaneously consider missing values and quantitative changes, which we combined with well-performing statistical tests for high confidence detection of differentially regulated features. The package contains functions to run the test and to visualize the results.

Authors:Veit Schwämmle [aut, cre]

PolySTest_1.1.0.tar.gz
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PolySTest_1.1.0.tgz(r-4.4-any)
PolySTest_1.1.0.tar.gz(r-4.5-noble)PolySTest_1.1.0.tar.gz(r-4.4-noble)
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PolySTest.pdf |PolySTest.html
PolySTest/json (API)
NEWS

# Install 'PolySTest' in R:
install.packages('PolySTest', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/computproteomics/polystest/issues

Datasets:

On BioConductor:PolySTest-1.1.0(bioc 3.21)PolySTest-0.99.6(bioc 3.20)

massspectrometryproteomicssoftwaredifferentialexpression

5.00 score 10 scripts 46 downloads 28 exports 130 dependencies

Last updated 29 days agofrom:43fe0683a5. Checks:OK: 1 NOTE: 2 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-winERRORNov 23 2024
R-4.5-linuxNOTENov 23 2024
R-4.4-winERRORNov 23 2024
R-4.4-macNOTENov 23 2024

Exports:check_for_polystestcheck_stat_namescreate_pairwise_comparisonsFindFCandQlimFindFCandQlimAlternativeget_numthreadslimma_pairedlimma_unpairedMissingStatsMissingStatsDesignMissValPDistrperm_unpairedpermtest_pairedplotExpressionplotHeatmaplyplotPvalueDistrplotRegNumberplotUpsetplotVolcanoPolySTest_pairedPolySTest_unpairedrp_unpairedRPStatsset_mfrowStatsForPermutTestttest_pairedttest_unpairedupdate_conditions_with_lcs

Dependencies:abindaskpassassertthatbase64encBiobaseBiocGenericsbitopsbslibcacachemcallrcaToolscirclizecliclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDelayedArraydendextenddigestdplyreggevaluatefansifarverfastmapfdrtoolfontawesomeforeachfsgclusgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2GlobalOptionsgluegplotsgridExtragtablegtoolsheatmaplyhighrhtmltoolshtmlwidgetshttpuvhttrIRangesisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplotlyplyrprocessxpromisespspurrrqapqvalueR6rappdirsRColorBrewerRcppregistryreshape2rlangrmarkdownS4ArraysS4VectorssassscalesseriationshapeshinysourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexTSPUCSC.utilsUpSetRutf8vctrsveganviridisviridisLitewebshotwithrxfunxtableXVectoryamlzlibbioc

Statistical testing of quantitative omics data

Rendered fromStatisticalTest.Rmdusingknitr::rmarkdownon Nov 23 2024.

Last update: 2024-06-12
Started: 2024-03-08

Readme and manuals

Help Manual

Help pageTopics
Check SummarizedExperiment for PolySTest Requirementscheck_for_polystest
Check Statistical Test and Comparison Namescheck_stat_names
Create All Pairwise Comparisonscreate_pairwise_comparisons
Function to determine "optimal" fold-change and q-value thresholds using a higher criticism method and an FC threshold based on a standard deviation of oneFindFCandQlimAlternative
Set number of threads (default is 4)get_numthreads
Perform paired limma analysislimma_paired
Perform unpaired limma analysislimma_unpaired
Example data set liver_example for PolySTestliver_example
Calculates the p-values and q-values for missing values in a data frame with columns as samples and rows as features.MissingStats
Function of calculation of Miss tests. This happens between full groups and thus does not have distinction for pairwise testing.MissingStatsDesign
Calculate the distribution of missing valuesMissValPDistr
Perform unpaired permutation testsperm_unpaired
Perform permutation testspermtest_paired
Plot Expression ProfilesplotExpression
Heatmap Visualization with HeatmaplyplotHeatmaply
Plot P-Value DistributionsplotPvalueDistr
Plot Number of Regulated FeaturesplotRegNumber
Plot UpSetplotUpset
Plot Volcano Plots for PolySTest resultsplotVolcano
PolySTest for Paired TestsPolySTest_paired
PolySTest for unpaired testsPolySTest_unpaired
Perform unpaired rank products testrp_unpaired
RPStats FunctionRPStats
Set Graphics Layoutset_mfrow
Calculate statistics for permutation testStatsForPermutTest
Perform paired t-teststtest_paired
Perform unpaired t-tests on two datasetsttest_unpaired
Update Conditions with Longest Common Subsequenceupdate_conditions_with_lcs