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

## Documentation for package ‘PolySTest’ version 1.6.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calculate_qvalues | 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.
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