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

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Documentation for package ‘PolySTest’ version 1.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

check_for_polystest	Check SummarizedExperiment for PolySTest Requirements
check_stat_names	Check Statistical Test and Comparison Names
create_pairwise_comparisons	Create All Pairwise Comparisons
FindFCandQlimAlternative	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
get_numthreads	Set number of threads (default is 4)
limma_paired	Perform paired limma analysis
limma_unpaired	Perform unpaired limma analysis
liver_example	Example data set liver_example for PolySTest
MissingStats	Calculates the p-values and q-values for missing values in a data frame with columns as samples and rows as features.
MissingStatsDesign	Function of calculation of Miss tests. This happens between full groups and thus does not have distinction for pairwise testing.
MissValPDistr	Calculate the distribution of missing values
permtest_paired	Perform permutation tests
perm_unpaired	Perform unpaired permutation tests
plotExpression	Plot Expression Profiles
plotHeatmaply	Heatmap Visualization with Heatmaply
plotPvalueDistr	Plot P-Value Distributions
plotRegNumber	Plot Number of Regulated Features
plotUpset	Plot UpSet
plotVolcano	Plot Volcano Plots for PolySTest results
PolySTest_paired	PolySTest for Paired Tests
PolySTest_unpaired	PolySTest for unpaired tests
RPStats	RPStats Function
rp_unpaired	Perform unpaired rank products test
set_mfrow	Set Graphics Layout
StatsForPermutTest	Calculate statistics for permutation test
ttest_paired	Perform paired t-tests
ttest_unpaired	Perform unpaired t-tests on two datasets
update_conditions_with_lcs	Update Conditions with Longest Common Subsequence