mogsa: Multiple omics data integrative clustering and gene set analysis

Share:

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

Author
Chen Meng
Date of publication
None
Maintainer
Chen Meng <mengchen18@gmail.com>
License
GPL-2
Version
1.8.0

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)

Files in this package

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