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mogsa (version 1.6.4)

Multiple omics data integrative clustering and gene set analysis

Description

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

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Version

Version

1.6.4

License

GPL-2

Maintainer

Chen Meng

Last Published

February 15th, 2017

Functions in mogsa (1.6.4)

bootMbpca

Bootstrap mbpca to estimate the coherence of different data sets
getmgsa

get values in an object of class "mgsa".
NCI60_4array_supdata

supp data for Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
annotate.gs

Summary annotation information of a gene set
NCI60_4arrays

Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
pairwise.rv

pairwise RV coefficients.
moa-class

Class "moa"
moaCoef

Extract the loadings/coefficients from an object of class moa-class.
box.gs.feature

boxplot of gene set variables across all samples.
sup.moa

Projecting supplementary tables on object of class moa-class.
moa

Multiple omics data analysis using MFA or STATIS
prepSupMoa

Prepare sumpplementary tables for projection by sup.moa or mogsa.
mogsa-package

Multiple omics clustering and gene set analysis
softK

Soft-thresholding operator
moaScore

Extract global scores from an object of class moa-class.
msvd

SVD based algorithm to calculate block Score and global scores for mbpca.
nipalsSoftK

NIPALS algorithm with soft thresholding operator
moGap

Gap statistic for clustering latent variables in moa-class.
decompose.gs.ind

Data-wise or PC-wise decomposition of gene set scores for a single observation.
moa.sup-class

Class "moa.sup"
plotGS

Plot the gene set space
processOpt

preprocessing of input data in mbpca.
mgsa-class

Class "mgsa"
prepGraphite

Prepare pathway gene sets from graphite package
combine-methods

Combine two objects of class mgsa into one.
deflat

deflat function used by mbpca
GIS

calculate gene influential scores of genes in a gene set.
distMoa

Calculate the distance matrix from an object of class moa-class.
bootMbpcaK

An internal function called by bootMbpca.
plot-methods

~~ Methods for Function plot ~~
toMoa

convert mbpca result to moa-class
prepMsigDB

Conver gmt format file to a list
matpower

compute the power of a matrix
mbpca

Extension of PCA to analyze multiple data sets
decompose.gs.group

Data-wise or PC-wise decomposition of gene set scores for all observations.
wsvd

Weighted singular value decomposition (SVD)
mogsa

multiple omics data integration and gene set analysis