mseapca: Metabolite set enrichment analysis for factor loading in principal component analysis

Share:

This package provides functions for metabolite set enrichment analysis (MSEA) and principal component analysis (PCA), and converting metabolite set list from your own csv files or KEGG's tar.gz files to XML documents. This package is suitable for computation of MSEA for factor loading in PCA.

Author
Hiroyuki Yamamoto
Date of publication
2012-04-15 16:42:20
Maintainer
Hiroyuki Yamamoto <h.yama2396@gmail.com>
License
BSD
Version
1.0

View on CRAN

Man pages

csv2list
Convert metabolite set / csv to list
list2xml
Convert metabolite set / list to XML format
msea_ora
MSEA by over representation analysis
msea_sub
MSEA by Subramanian et al.
pathway_class
Convert metabolite set (multiple) / tar.gz to list
pca_scaled
PCA for autoscaled data
read_pathway
Read metabolite set file (*.xml)
setlabel
Generate binary label matrix of metabolite set

Files in this package

mseapca
mseapca/MD5
mseapca/sample
mseapca/sample/pathway.xml
mseapca/R
mseapca/R/setlabel.R
mseapca/R/read_pathway.R
mseapca/R/pca_scaled.R
mseapca/R/pathway_class.R
mseapca/R/msea_sub.R
mseapca/R/msea_ora.R
mseapca/R/list2xml.R
mseapca/R/kgml_i.R
mseapca/R/csv2list.R
mseapca/NAMESPACE
mseapca/man
mseapca/man/setlabel.Rd
mseapca/man/read_pathway.Rd
mseapca/man/pca_scaled.Rd
mseapca/man/pathway_class.Rd
mseapca/man/msea_sub.Rd
mseapca/man/msea_ora.Rd
mseapca/man/list2xml.Rd
mseapca/man/csv2list.Rd
mseapca/DESCRIPTION