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mogsa (version 1.2.0)

Multiple omics data integration 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

1.2.0

License

GPL-2

Maintainer

Chen Meng

Last Published

February 15th, 2017

Functions in mogsa (1.2.0)

getmgsa

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

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

Class "moa.sup"
moaCoef

Extract the loadings/coefficients from an object of class moa-class.
bootMbpcaK

An internal function called by bootMbpca.
box.gs.feature

boxplot of gene set variables across all samples.
moaScore

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

Gap statistic for clustering latent variables in moa-class.
plotGS

Plot the gene set space
prepGraphite

Prepare pathway gene sets from graphite package
decompose.gs.ind

Data-wise or PC-wise decomposition of gene set scores for a single observation.
deflat

deflat function used by mbpca
moa

Multiple omics data analysis using MFA or STATIS
moa-class

Class "moa"
msvd

SVD based algorithm to calculate block Score and global scores for mbpca.
NCI60_4array_supdata

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

Prepare sumpplementary tables for projection by sup.moa or mogsa.
prepMsigDB

Conver gmt format file to a list
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.
mbpca

Extension of PCA to analyze multiple data sets
mgsa-class

Class "mgsa"
NCI60_4arrays

Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
nipalsSoftK

NIPALS algorithm with soft thresholding operator
sup.moa

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

convert mbpca result to moa-class
annotate.gs

Summary annotation information of a gene set
bootMbpca

Bootstrap mbpca to estimate the coherence of different data sets
pairwise.rv

pairwise RV coefficients.
processOpt

preprocessing of input data in mbpca.
plot-methods

~~ Methods for Function plot ~~
softK

Soft-thresholding operator
GIS

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

compute the power of a matrix
mogsa-package

Multiple omics gene set analysis
mogsa

multiple omics data integration and gene set analysis
wsvd

Weighted singular value decomposition (SVD)