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

## Documentation for package ‘OMICsPCA’ version 1.8.0

- 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