# Multiple omics data integrative clustering and gene set analysis

## Documentation for package ‘mogsa’ version 1.42.0

- 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)