Multiple omics data integrative clustering and gene set analysis

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Documentation for package ‘mogsa’ version 1.41.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

mogsa-package	Multiple omics clustering and gene set analysis
annotate.gs	Summary annotation information of a gene set
biSoftK	NIPALS algorithm with soft thresholding operator on rows and columns
bootMbpca	Bootstrap mbpca to estimate the coherence of different data sets
bootMbpcaK	An internal function called by 'bootMbpca'.
bootMoa	Significant components in "moa" returned by function "moa".
box.gs.feature	boxplot of gene set variables across all samples.
combine	Combine two objects of class 'mgsa' into one.
combine-method	Combine two objects of class 'mgsa' into one.
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 observations.
decompose.gs.ind	Data-wise or PC-wise decomposition of gene set scores for a single observation.
deflat	deflat function used by 'mbpca'
distMoa	Calculate the distance matrix from an object of class 'moa-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"'
moa.sup-class	Class '"moa.sup"'
moaCoef	Extract the loadings/coefficients from an object of class 'moa-class'.
moaScore	Extract global scores from an object of class 'moa-class'.
moGap	Gap statistic for clustering latent variables in 'moa-class'.
mogsa	multiple omics data integration and gene set analysis
msvd	SVD based algorithm to calculate block Score and global scores for 'mbpca'.
NCI60_4arrays	Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
NCI60_4array_supdata	supp data for Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
nipalsSoftK	NIPALS algorithm with soft thresholding operator
pairwise.rv	pairwise RV coefficients.
plot-method	Class '"moa"'
plot-methods	Methods for function 'plot'
plotGS	Plot the gene set space
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 mogsa.
print	Methods for function 'print'
print-method	Methods for function 'print'
print-methods	Methods for function 'print'
processOpt	preprocessing of input data in 'mbpca'.
show	Methods for function 'show'
show-method	Methods for function 'show'
show-methods	Methods for function 'show'
softK	Soft-thresholding operator
summary	Methods for function 'summary'
summary-method	Methods for function 'summary'
summary-methods	Methods for function 'summary'
sup.moa	Projecting supplementary tables on object of class 'moa-class'.
toMoa	convert 'mbpca' result to 'moa-class'
wsvd	Weighted singular value decomposition (SVD)