mogsa: Multiple omics data integrative clustering and gene set analysis

This package provide a method for doing gene set analysis based on multiple omics data.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mogsa")
AuthorChen Meng
Bioconductor views Clustering GeneExpression PrincipalComponent Software StatisticalMethod
Date of publicationNone
MaintainerChen Meng <mengchen18@gmail.com>
LicenseGPL-2
Version1.10.0

View on Bioconductor

Man pages

annotate.gs: Summary annotation information of a gene set

bootMbpca: Bootstrap mbpca to estimate the coherence of different data...

bootMbpcaK: An internal function called by 'bootMbpca'.

box.gs.feature: boxplot of gene set variables across all samples.

combine-methods: Combine two objects of class 'mgsa' into one.

decompose.gs.group: Data-wise or PC-wise decomposition of gene set scores for all...

decompose.gs.ind: Data-wise or PC-wise decomposition of gene set scores for a...

deflat: deflat function used by 'mbpca'

distMoa: Calculate the distance matrix from an object of class...

getmgsa: get values in an object of class "mgsa".

GIS: calculate gene influential scores of genes in a gene set.

matpower: compute the power of a matrix

mbpca: Extension of PCA to analyze multiple data sets

mgsa-class: Class '"mgsa"'

moa: Multiple omics data analysis using MFA or STATIS

moa-class: Class '"moa"'

moaCoef: Extract the loadings/coefficients from an object of class...

moaScore: Extract global scores from an object of class 'moa-class'.

moa.sup-class: Class '"moa.sup"'

moGap: Gap statistic for clustering latent variables in 'moa-class'.

mogsa: multiple omics data integration and gene set analysis

mogsa-package: Multiple omics clustering and gene set analysis

msvd: SVD based algorithm to calculate block Score and global...

NCI60_4arrays: Microarray gene expression profiles of the NCI 60 cell lines...

NCI60_4array_supdata: supp data for Microarray gene expression profiles of the NCI...

nipalsSoftK: NIPALS algorithm with soft thresholding operator

pairwise.rv: pairwise RV coefficients.

plotGS: Plot the gene set space

plot-methods: Methods for function 'plot'

prepGraphite: Prepare pathway gene sets from graphite package

prepMsigDB: Conver gmt format file to a list

prepSupMoa: Prepare sumpplementary tables for projection by sup.moa or...

print-methods: Methods for function 'print'

processOpt: preprocessing of input data in 'mbpca'.

show-methods: Methods for function 'show'

softK: Soft-thresholding operator

summary-methods: Methods for function 'summary'

sup.moa: Projecting supplementary tables on object of class...

toMoa: convert 'mbpca' result to 'moa-class'

wsvd: Weighted singular value decomposition (SVD)

Functions

annotate.gs Man page
bootMbpca Man page
bootMbpcaK Man page
box.gs.feature Man page
combine Man page
combine-methods Man page
combine,mgsa,mgsa-method Man page
decompose.gs.group Man page
decompose.gs.ind Man page
deflat Man page
distMoa Man page
getmgsa Man page
GIS Man page
matpower Man page
mbpca Man page
mgsa-class Man page
moa Man page
moa-class Man page
moaCoef Man page
moaScore Man page
moa.sup-class Man page
moGap Man page
mogsa Man page
mogsa Man page
mogsa-package Man page
msvd Man page
NCI60_4arrays Man page
NCI60_4array_supdata Man page
nipalsSoftK Man page
pairwise.rv Man page
plotGS Man page
plot-methods Man page
plot,moa,missing-method Man page
prepGraphite Man page
prepMsigDB Man page
prepSupMoa Man page
print Man page
print-methods Man page
print,mgsa-method Man page
print,moa-method Man page
print,moa.sup-method Man page
processOpt Man page
show Man page
show-methods Man page
show,mgsa-method Man page
show,moa-method Man page
show,moa.sup-method Man page
softK Man page
summary Man page
summary-methods Man page
summary,mgsa-method Man page
summary,moa-method Man page
summary,moa.sup-method Man page
sup.moa Man page
toMoa Man page
wsvd Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllMethods.R R/GIS.R R/bootMbpca.R R/bootMbpcaK.R R/box.gs.R R/combine.mogsa.R R/decompose.gs.group.R R/decompose.gs.ind.R R/deflat.R R/distMoa.R R/getmgsa.R R/ks.stat.R R/matpower.R R/mbpca.R R/moGap.R R/moa.R R/moaExtract.R R/mogsa.R R/msvd.R R/nipalsSoftK.R R/pairwise.rv.R R/plotGS.R R/preGeneSet.R R/preprocess.data.R R/print.summary.R R/processOpt.R R/softK.R R/sup.moa.R R/toMoa.R R/wsvd.R
build
build/vignette.rds
data
data/NCI60_4array_supdata.rda
data/NCI60_4arrays.rda
inst
inst/NEWS
inst/doc
inst/doc/moCluster.R
inst/doc/moCluster.Rnw
inst/doc/moCluster.pdf
inst/doc/mogsa.R
inst/doc/mogsa.Rnw
inst/doc/mogsa.pdf
inst/extdata
inst/extdata/example_msigdb_data.gmt.gz
man
man/GIS.Rd man/NCI60_4array_supdata.Rd man/NCI60_4arrays.Rd man/annotate.gs.Rd man/bootMbpca.Rd man/bootMbpcaK.Rd man/box.gs.feature.Rd man/combine-methods.Rd man/decompose.gs.group.Rd man/decompose.gs.ind.Rd man/deflat.Rd man/distMoa.Rd man/getmgsa.Rd man/matpower.Rd man/mbpca.Rd man/mgsa-class.Rd man/moGap.Rd man/moa-class.Rd man/moa.Rd man/moa.sup-class.Rd man/moaCoef.Rd man/moaScore.Rd man/mogsa-package.Rd man/mogsa.Rd man/msvd.Rd man/nipalsSoftK.Rd man/pairwise.rv.Rd man/plot-methods.Rd man/plotGS.Rd man/prepGraphite.Rd man/prepMsigDB.Rd man/prepSupMoa.Rd man/print-methods.Rd man/processOpt.Rd man/show-methods.Rd man/softK.Rd man/summary-methods.Rd man/sup.moa.Rd man/toMoa.Rd man/wsvd.Rd
vignettes
vignettes/moCluster.Rnw
vignettes/mogsa.Rnw
vignettes/mogsa.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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