getPCAs: Principal component analysis of samples from ExpressionSet or...

In msuprun/bbeaR: an R package and framework for epitope-specific antibody profiling

Description

A wrapper function of the stats::prcomp that takes an ExpressionSet or a matrix, calculates principal comonents, and merges the results with phenotype/clinical data (from ExpressionSet object).

Usage

getPCAs(eset, maxpc = 3)

Arguments

eset	expressionSet or matrix of the epitope data, where samples are columns, and features are rows
maxpc	number of principal components in the output

Value

The function returns a list object with a data.frame, which consists of pricincipal components and phenotypic data (if eset instead of matrix was provided), and varex - proportion of variance explained by each component.

Author(s)

Maria Suprun, Randall J. Ellis, Mayte Suárez-Fariñas

Examples

data(Egg)
pca.db <- getPCAs(as.matrix(bbea$Median), maxpc = 3)
head(pca.db$db)
pca.db$varex

msuprun/bbeaR documentation built on Jan. 31, 2021, 6:49 p.m.