integrate_variables: Integration of an experiment/ Assay done on many Cell lines/...

Description Usage Arguments Value Author(s) Examples

View source: R/integrate_variables.R

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

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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

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

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