# Shiny-based interactive data-quality exploration for omics data

## Documentation for package ‘MatrixQCvis’ version 1.18.0

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

## Help Pages

barplotSamplesMeasuredMissing | Barplot of number of measured/missing features of samples
batchCorrectionAssay | Remove batch effects from (count/intensity) values of a 'SummarizedExperiment'
createBoxplot | Create a boxplot of (count/intensity) values per sample
createDfFeature | Create data frame of (count/intensity) values for a selected feature along data processing steps
cv | Calculate coefficient of variation
cvFeaturePlot | Plot of feature-wise coefficient of variation values
dimensionReduction | Dimensionality reduction with dimensionReduction methods PCA, PCoA, NMDS, UMAP and tSNE
dimensionReductionPlot | Plot the coordinates from 'dimensionReduction' values
distSample | Create a heatmap using distance information between samples
distShiny | Create distance matrix from numerical matrix
driftPlot | Plot the trend line for aggregated values
ECDF | Create ECDF plot of a sample against a reference
explVar | Retrieve the explained variance for each principal component (PCA) or axis (PCoA)
extractComb | Obtain the features that are present in a specified set
featurePlot | Create a plot of (count/intensity) values over the samples
histFeature | Histogram for measured value per feature
histFeatureCategory | Histogram of features per sample type
hist_sample | Plot a histogram of the number of a category
hist_sample_num | Return the number of a category
hoeffDPlot | Create a plot from a list of Hoeffding's D values
hoeffDValues | Create values of Hoeffding's D statistics from M and A values
imputeAssay | Impute missing values in a 'matrix'
MAplot | Create a MA plot
MAvalues | Create values (M and A) for MA plot
measuredCategory | Obtain the number of measured intensities per sample type
mosaic | Mosaic plot for two factors in colData(se)
normalizeAssay | Normalize a data sets (reduce technical sample effects)
permuteExplVar | Permute the expression values and retrieve the explained variance
plotCV | Plot CV values
plotPCALoadings | Plot for PCA loadings of features
plotPCAVar | Plot of explained variance against the principal components
plotPCAVarPvalue | Plot p-values for the significance of principal components
samplesMeasuredMissing | Create tibble containing number of measured/missing features of samples
shinyQC | Shiny application for initial QC exploration of -omics data sets
sumDistSample | Plot the sum of distances to other samples
tblPCALoadings | Return tibble with PCA loadings for features
transformAssay | Transform the (count/intensity) values of a 'data.frame', 'tbl' or 'matrix'
upsetCategory | UpSet plot to display measures values across sample types
volcanoPlot | Volcano plot of fold changes/differences against p-values