Package: PolySTest 1.7.0

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_1.7.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PolySTest/json (API)

# Install 'PolySTest' in R:

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

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

Datasets:

liver_example - Example data set liver_example for PolySTest

On BioConductor:PolySTest-1.7.0(bioc 3.24)PolySTest-1.6.0(bioc 3.23)

massspectrometry proteomics software differentialexpression csv differential-protein-expression-profiling dsv expression-data gene-expression-profile heat-map histogram p-value proteomics-experiment q-value statistical-modelling statistics-and-probability svg

4.40 score 10 scripts 268 downloads 29 exports 122 dependencies

Last updated from:92e6451639. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	191
linux-devel	NOTE	551
source / vignettes	OK	311
linux-release	NOTE	575
macos-release	NOTE	479
macos-oldrel	NOTE	375
windows-devel	NOTE	298
windows-release	NOTE	418
windows-oldrel	NOTE	423
wasm-release	OK	145

Exports:calculate_qvalues check_for_polystest check_stat_names create_pairwise_comparisons FindFCandQlim FindFCandQlimAlternative get_numthreads limma_paired limma_unpaired MissingStats MissingStatsDesign MissValPDistr perm_unpaired permtest_paired plotExpression plotHeatmaply plotPvalueDistr plotRegNumber plotUpset plotVolcano PolySTest_paired PolySTest_unpaired rp_unpaired RPStats set_mfrow StatsForPermutTest ttest_paired ttest_unpaired update_conditions_with_lcs

Dependencies:abind askpass assertthat base64enc Biobase BiocGenerics bitops bslib ca cachem callr caTools circlize cli cluster codetools colorspace commonmark cpp11 crosstalk curl data.table DelayedArray dendextend digest dplyr egg evaluate farver fastmap fdrtool fontawesome foreach fs gclus generics GenomicRanges ggplot2 GlobalOptions glue gplots gridExtra gtable gtools heatmaply highr htmltools htmlwidgets httpuv httr IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly plyr processx promises ps purrr qap qvalue R6 rappdirs RColorBrewer Rcpp registry reshape2 rlang rmarkdown S4Arrays S4Vectors S7 sass scales Seqinfo seriation shape shiny sourcetools SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex TSP UpSetR utf8 vctrs viridis viridisLite webshot withr xfun xtable XVector yaml

Statistical testing of quantitative omics data

Rendered fromStatisticalTest.Rmdusingknitr::rmarkdown

Last update: 2024-12-31
Started: 2024-03-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate FDRs for a given vector of p-values with qvalue, fallback to BH adjustment if qvalue fails. Default to BH in case of less than 200 p-values.	calculate_qvalues
Check SummarizedExperiment for PolySTest Requirements	check_for_polystest
Check Statistical Test and Comparison Names	check_stat_names
Create All Pairwise Comparisons	create_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 one	FindFCandQlimAlternative
Set number of threads (default is 4)	get_numthreads
Perform paired limma analysis	limma_paired
Perform unpaired limma analysis	limma_unpaired
Example data set liver_example for PolySTest	liver_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 values	MissValPDistr
Perform unpaired permutation tests	perm_unpaired
Perform permutation tests	permtest_paired
Plot Expression Profiles	plotExpression
Heatmap Visualization with Heatmaply	plotHeatmaply
Plot P-Value Distributions	plotPvalueDistr
Plot Number of Regulated Features	plotRegNumber
Plot UpSet	plotUpset
Plot Volcano Plots for PolySTest results	plotVolcano
PolySTest for Paired Tests	PolySTest_paired
PolySTest for unpaired tests	PolySTest_unpaired
Perform unpaired rank products test	rp_unpaired
RPStats Function	RPStats
Set Graphics Layout	set_mfrow
Calculate statistics for permutation test	StatsForPermutTest
Perform paired t-tests	ttest_paired
Perform unpaired t-tests on two datasets	ttest_unpaired
Update Conditions with Longest Common Subsequence	update_conditions_with_lcs