CSFA: Connectivity Scores with Factor Analysis
Version 0.91

Applies Factor Analysis methodology to microarray data in order to derive connectivity scores between compounds. The package also contains an implementation of the Connectivity Score algorithm by Zhang and Gant.

Browse man pages Browse package API and functions Browse package files

AuthorEwoud De Troyer
Date of publication2016-09-19 12:53:22
MaintainerEwoud De Troyer <ewoud.detroyer@uhasselt.be>
LicenseGPL-3
Version0.91
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("CSFA", repos="http://R-Forge.R-project.org")

Man pages

CSanalysis: Connectivity Score Analysis.
CSanalysis-matrix-matrix-character-method: Connectivity Score Analysis.
CSanalysis-matrix-matrix-CSfabia-method: "CSfabia"
CSanalysis-matrix-matrix-CSmfa-method: "CSmfa"
CSanalysis-matrix-matrix-CSpca-method: "CSpca"
CSanalysis-matrix-matrix-CSsmfa-method: "CSsmfa"
CSanalysis-matrix-matrix-CSzhang-method: "CSzhang"
CScompare: Compare CS Results.
CSFA: Computing connectivity scores with Factor Analysis...
CSlabelscompare: Compare Automatic Factor Labels with Manual Provided Labels.
CSpermute: Permute CS results
CSresult-class: An S4 class in which the results of the Connectivity Scores...
dataSIM: Simulated Microarray Data

Functions

CSFA Man page
CSFA-package Man page
CSanalysis Man page
CSanalysis,matrix,matrix,CSfabia-method Man page
CSanalysis,matrix,matrix,CSmfa-method Man page
CSanalysis,matrix,matrix,CSpca-method Man page
CSanalysis,matrix,matrix,CSsmfa-method Man page
CSanalysis,matrix,matrix,CSzhang-method Man page
CSanalysis,matrix,matrix,character-method Man page
CScompare Man page Source code
CSgrouploadings Source code
CSlabelscompare Man page Source code
CSpermute Man page Source code
CSprofiles Source code
CSrank2 Source code
CSresult-class Man page
analyse_FA Source code
analyse_FA2 Source code
analyse_zhang Source code
compare.CS.plot Source code
compare.CSRank.plot Source code
compare.GS.plot Source code
compare.pvalues.plot Source code
compare_CS_CSRankScores Source code
dataSIM Man page
fabia.overlap Source code
get.CS.GS Source code
get.loadings Source code
getWeightedDat Source code
plot_contributions Source code
pvalue2_compare Source code
pvalue_compute Source code
pvalue_hist Source code
pvalue_volc Source code
threshSamp Source code
zhangscore Source code
zhangscore.support Source code

Files

DESCRIPTION
NAMESPACE
R
R/CSFA.R
R/CScompare.R
R/analyse_functions.R
R/extra.R
R/fabia_functions.R
R/method_structure.R
R/permutation_functions.R
R/zhang_functions.R
build
build/vignette.rds
data
data/dataSIM.RData
data/datalist
inst
inst/doc
inst/doc/CSFA.Rnw
inst/doc/CSFA.pdf
man
man/CSFA.Rd
man/CSanalysis-matrix-matrix-CSfabia-method.Rd
man/CSanalysis-matrix-matrix-CSmfa-method.Rd
man/CSanalysis-matrix-matrix-CSpca-method.Rd
man/CSanalysis-matrix-matrix-CSsmfa-method.Rd
man/CSanalysis-matrix-matrix-CSzhang-method.Rd
man/CSanalysis-matrix-matrix-character-method.Rd
man/CSanalysis.Rd
man/CScompare.Rd
man/CSlabelscompare.Rd
man/CSpermute.Rd
man/CSresult-class.Rd
man/dataSIM.Rd
vignettes
vignettes/CSFA.Rnw
vignettes/asa.bst
vignettes/connectivityRef.bib
vignettes/figure
vignettes/figure/CScompare-1.pdf
vignettes/figure/CScompare-2.pdf
vignettes/figure/CScompare-3.pdf
vignettes/figure/CScompare-4.pdf
vignettes/figure/CScompare-5.pdf
vignettes/figure/CSpermuteplots-1.pdf
vignettes/figure/CSpermuteplots-2.pdf
vignettes/figure/CSpermuteplots-3.pdf
vignettes/figure/CSpermuteplots2-1.pdf
vignettes/figure/CSpermuteplots2-2.pdf
vignettes/figure/CSpermuteplots2-3.pdf
vignettes/figure/FABIA-1.pdf
vignettes/figure/FABIA-2.pdf
vignettes/figure/FABIA-3.pdf
vignettes/figure/MFA-1.pdf
vignettes/figure/MFA-2.pdf
vignettes/figure/MFA-3.pdf
vignettes/figure/MFA-4.pdf
vignettes/figure/MFA2-1.pdf
vignettes/figure/MFA3-1.pdf
vignettes/figure/ZG-1.pdf
vignettes/figure/data_heatmap-1.png
vignettes/perm_data
vignettes/perm_data/out_MFA.RData
vignettes/perm_data/out_ZG.RData
CSFA documentation built on May 21, 2017, 3:30 a.m.