An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

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Documentation for package ‘OMICsPCA’ version 1.27.0

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

Help Pages

analyse_individuals	Quick analysis and visualization of the individuals/annotations/rows (e.g. Tss, gene) from integrated Assay.
analyse_integrated_individuals	Quick analysis and visualization of the individuals/annotations/rows (e.g. Tss, gene)
analyse_integrated_variables	Quick analysis and visualization of the integrated Assays by integrate() function.
analyse_variables	Quick analysis and visualization of the integrated Assays by integrate() function.
chart_correlation	Pairwise correlation, scatter plot and histogram on selected groups.
cluster	Cluster data points
cluster_boxplot	Comparison of clusters by boxplot
cluster_parameters	Detection of algorithm and number of clusters
create_group	Subsets an Assay dataframe into smaller groups
descriptor	Distribution of Assays as percentage of cell lines
extract	extraction of projected cooordinates from "PCA" object.
extract_assay	Data extraction from "MultiAssayExperiment" object
integrate_pca	Integration of multiple Assays into linear combinations by PCA.
integrate_variables	Integration of an experiment/ Assay done on many Cell lines/ time points into linear combinations by PCA.
intersect	support function of prepareDataset
merge_cells	Storage of intersected factors from multiple cell types as columns into a dataframe
plot_density	Visualization of Density of various groups on Principal components
plot_density_3D	Visualization of 3D Density of various groups on Principal components
plot_integrated_density	Visualization of Density of various groups on Principal components of integrated assays
plot_integrated_density_3D	Visualization of 3D Density of various groups on Principal components of multiple Assays
prepare_dataset	Intersects and merge data from multiple experiments into a dataframe