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.

AuthorChen Meng
Date of publicationNone
MaintainerChen Meng <mengchen18@gmail.com>
LicenseGPL-2
Version1.8.0

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...

processOpt: preprocessing of input data in 'mbpca'.

softK: Soft-thresholding operator

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
plot,moa,missing-method Man page
prepGraphite Man page
prepMsigDB Man page
prepSupMoa Man page
processOpt Man page
softK Man page
sup.moa Man page
toMoa Man page
wsvd Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.