analyse_integrated_variables: Quick analysis and visualization of the integrated Assays by...

In subhadeep1024/OMICsPCA: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

Description

This function is designed for a quick analysis and visualization of the data integrated by "integrateAssays()"" function. It works similarly as analyse_variables. In addition to that it takes an additinal argument "start_end" returned by "integrateAssays()".

Usage

analyse_integrated_variables(start_end = start_end, Assay = "all",
name, choice, title = NULL, PC = 1,
var_type = "contrib", ...)

Arguments

start_end	a list as returned by "integrate_pca()"
Assay	Name of an Assay. default = "all"
name	Name of the "PCA" object returned by "integrate_pca()"
choice	1 = variance barplot 2 = Loadings of cell lines on selected PCs 3 = hCorrelation matrix 4 = Squarred loadings of Cell lines on a PC 5 = Contribution of Cell lines on a PC for details of the choices see the vignette
title	title of plots
PC	The PC on which the plots will be drawn. used in choice 4 and 5. default = 1
var_type	Used when choice = 2. available options are: "coord", "cos2" and "contrib"
...	additional arguments allowed to base functions "used in various choices. See vignettes for details.

Value

Displays various plots and tables as per the combination of input arguments

Author(s)

Subhadeep Das <[e-mail]>

Examples

exclude <- list(0,c(1,9))

int_PCA <- integrate_pca(Assays = c("H2az",
"H3k9ac"), name = multi_assay, mergetype = 2,
exclude = exclude, graph = FALSE)

start_end = int_PCA$start_end

name = int_PCA$int_PCA


analyse_integrated_variables(start_end = start_end, name = name,
choice = 1, title = "variance barplot", Assay = 1, addlabels = TRUE)

subhadeep1024/OMICsPCA documentation built on March 17, 2020, 5:23 p.m.