leverage-pcaRes-method: Extract leverages of a PCA model

In pcaMethods: A collection of PCA methods

Description

The leverages of PCA model indicate how much influence each observation has on the PCA model. Observations with high leverage has caused the principal components to rotate towards them. It can be used to extract both "unimportant" observations as well as picking potential outliers.

Usage

## S4 method for signature 'pcaRes'
leverage(object)

Arguments

object

a pcaRes object

Details

Defined as Tr(T(T'T)^(-1)T')

Value

The observation leverages as a numeric vector

Author(s)

Henning Redestig

References

Introduction to Multi- and Megavariate Data Analysis using Projection Methods (PCA and PLS), L. Eriksson, E. Johansson, N. Kettaneh-Wold and S. Wold, Umetrics 1999, p. 466

Examples

data(iris)
pcIr <- pca(iris[,1:4])
## versicolor has the lowest leverage
with(iris, plot(leverage(pcIr)~Species))

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'pcaMethods'

The following object is masked from 'package:stats':

    loadings

pcaMethods documentation built on Nov. 8, 2020, 6:19 p.m.