extract: extraction of projected cooordinates from "PCA" object.

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

Description

funtion to extract projected coordinates of individuals on principal components.

Usage

extract(name, groups, integrated = TRUE, Assay = NULL,
rand = NULL, PC = c(1,2,3,4), groupinfo = NULL)

Arguments

name	name of the OMICs object.
groups	one or more groups created by or supplied through "create_group()"
integrated	whether to extract coordinates from integrated or individual assay.
Assay	name of the assay if integrated = FALSE
rand	number of rows to be extracted randomly.
PC	principal component numbers. The projected informaton on this PCs will be extracted.
groupinfo	same as integrate_variables()

Value

a data frame of the extracted value.

Author(s)

Subhadeep Das

Examples

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

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

name = int_PCA$int_PCA

data <- extract(name = name, PC = c(1:4),
groups = c("WE","RE"), integrated = TRUE, rand = 600,
groupinfo = groupinfo_ext)

OMICsPCA documentation built on Nov. 8, 2020, 5:01 p.m.