PCanalysis: PC analysis on numerical DNA sequences

In MEET: MEET: Motif Elements Estimation Toolkit

Description

Performs a PC analysis of numerical DNA sequences, using the pcaMethods package and projects the studied DNA sequence to the subspace. The Q-residuals (euclidean distance between the sequences and the modeled subspace) of the DNA studied sequence are returned as output.

Usage

PCanalysis(TFBS, nPCs, Sequences)

Arguments

TFBS	DNA numerical matrix of known TFBS
nPCs	Number of principal components used to build the model
Sequences	numerical matrix of DNA sequences to study (converted as a numerical matrix)

Value

residus: Euclidean distance from the studied sequences to the modeled motif

Author(s)

Erola Pairo <[e-mail]>

References

Jolliffe I.T. Principal Component Analysis, Series: Springer Series in Statistics, 2nd ed., Springer, NY, 2002, XXIX, 487 p. 28 illus. ISBN 978-0-387-95442-4

Stacklies, Wolfram, Redestig, Henning, Scholz, Matthias, Walther, Dirk, and Selbig, Joachim: pcaMethods a bioconductor package providing PCA methods for incomplete data, Bioinformatics 23(9), 1164, 2007

See Also

PCA, kfold.PCA

Examples

data(numericalTF)
nPCs<-3
solution<-PCanalysis(TFBS=numericalDNA, nPCs=nPCs, numericalDNA)

MEET documentation built on May 2, 2019, 5:52 p.m.