Shiny-based interactive data-quality exploration for omics data


[Up] [Top]

Documentation for package ‘MatrixQCvis’ version 1.4.0

Help Pages

barplotSamplesMeasuredMissing Barplot of number of measured/missing features of samples
batchCorrectionAssay Remove batch effects from (count/intensity) values of a 'SummarizedExperiment'
biocrates Convert Biocrates xlsx output to 'SummarizedExperiment' object
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
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
maxQuant Convert MaxQuant xlsx output to 'SummarizedExperiment' object
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)
ordination Dimensionality reduction with ordination methods PCA, PCoA, NMDS, UMAP and tSNE
ordinationPlot Plot the coordinates from 'ordination' values
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
spectronaut Convert Spectronaut xlsx output to 'SummarizedExperiment' object
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