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) |