Multiple omics data integration and gene set analysis


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Documentation for package ‘mogsa’ version 1.0.3

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mogsa-package Multiple omics gene set analysis
annotate.gs Summary annotation information of a gene set
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.
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
mgsa-class Class '"mgsa"'
moa Multiple omics data analysis using MFA or STATIS
moa-class Class '"moa"'
moa.sup-class Class '"moa.sup"'
mogsa multiple omics data integration and gene set analysis
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
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.
sup.moa Projecting supplementary tables on object of class 'moa-class'.
wsvd Weighted singular value decomposition (SVD)