integrate_variables {OMICsPCA} | R Documentation

## Integration of an experiment/ Assay done on many Cell lines/ time points into linear combinations by PCA.

### Description

If an assay (e.g. ChIP-seq for the histone modification H3k9ac) is done on multiple cells/conditions/treatment/time, it might be, sometimes, necessary to integrate or combine them. Such combination may be done by several techniques like Principal Component Analysis (PCA) or Factor Analysis (FA). This function integrates an assay experimented on multiple cells or conditions into many linear combinations using PCA.

### Usage

    integrate_variables(Assays, name, groups, groupinfo = NULL, ...)

### Arguments

`Assays` | A vector of names of an assays
`name` | Name of the "MultiAssayExperiment" object containing the assay data
`groups` | Name of all or subset of groups
`groupinfo` | output of create_group or similar object containing group information
`...` | Additional arguments supplied to "PCA()" imported from "FactoMineR"

### Value

an object of class "PCA"

### Author(s)

Subhadeep Das <subhadeep1024@gmail.com>

### Examples

    PCAlist <- integrate_variables(Assays = c("H2az","H3k4me1",
    "H3k9ac"), name = multi_assay,
    groups = c("WE","RE"), groupinfo = groupinfo_ext,
    scale.unit = FALSE, graph = FALSE)

[Package OMICsPCA version 1.4.0 Index]