Package: R.ComDim 1.0.0

Francesc Puig-Castellví

R.ComDim: Common Dimensions (ComDim) Multi-Block Analysis

Common Dimensions (ComDim) is a multi-block method that simultaneously considers multiple data tables to find latent components that are common to all the tables as well as those specific to each data table, along with the contribution of each table to each component. See Jouan-Rimbaud Bouveresse and Rutledge (2024) <doi:10.1002/cem.3454>, Boccard and Rutledge (2013) <doi:10.1016/j.aca.2013.01.022>, and Puig-Castellví et al. (2021) <doi:10.1016/j.chemolab.2021.104422>.

Authors:Francesc Puig-Castellví [aut, cre]

R.ComDim_1.0.0.tar.gz
R.ComDim_1.0.0.tar.gz(r-4.7-any)R.ComDim_1.0.0.tar.gz(r-4.6-any)
R.ComDim_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
R.ComDim/json (API)

# Install 'R.ComDim' in R:
install.packages('R.ComDim', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • extra - Extracellular metabolites in growth medium
  • gcms - GCMS data on cell differentiation
  • intra - Intracellular metabolites in growth medium
  • KEGG_table_metabolites - Metadata for the metabolites in growth medium
  • lcms - LCMS data on cell differentiation
  • lipids - Lipid profiles of cell extracts
  • metadata_lipids - Metadata for the lipid profiles of cell extracts
  • metadata_RNAseq3 - Metadata for the RNAseq data of cell extracts
  • mirnaseq - MiRNAseq data on cell differentiation
  • rnaseq - RNAseq data on cell differentiation
  • RNAseq3 - RNAseq data of cell extracts

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 31 exports 25 dependencies

Last updated from:d6b7a04420. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK151
source / vignettesOK185
linux-release-x86_64OK160
wasm-releaseOK127

Exports:AddMetadatablockNamesblockNames<-ComDim_ExploratoryComDim_OPLSComDim_PCAComDim_PLSComDim_yExpandMultiBlockFilterSamplesMultiBlockMakeComDimLoadingsTableMakeComDimScoresTableMultiAssayExperiment2MultiBlockMultiBlockMultiBlock2MatrixMultiBlock2MultiAssayExperimentNAInfRemoveMultiBlockncolNormalizeMultiBlocknrowOPLS_NIPALS_DNRPredictMultiBlockProcessMultiBlocksampleNamessampleNames<-SelectFeaturesRWSimulateMultiBlockSplitRWSummarizedExperiment2MultiBlockvariableNamesvariableNames<-

Dependencies:cliConsensusOPLScpp11farverggplot2gluegtableisobandlabelinglifecyclemagrittrplyrpracmaR6RColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
AddMetadataAddMetadata
blockNamesblockNames blockNames,MultiBlock-method
blockNames<-blockNames<- blockNames<-,MultiBlock-method
ComDim_Exploratory - Extending matrix decomposition methods to multi-block data.ComDim_Exploratory
ComDim_OPLSComDim_OPLS
ComDim_PCAComDim_PCA
ComDim_PLSComDim_PLS
ComDim_y - Extending PLS-like supervised methods to multi-block data.ComDim_y
MultiBlock objectComDim ComDim-classes
ExpandMultiBlockExpandMultiBlock
Extracellular metabolites in growth mediumextra
FilterSamplesMultiBlockFilterSamplesMultiBlock
GCMS data on cell differentiationgcms
Intracellular metabolites in growth mediumintra
Metadata for the metabolites in growth mediumKEGG_table_metabolites
LCMS data on cell differentiationlcms
Lipid profiles of cell extractslipids
MakeComDimLoadingsTableMakeComDimLoadingsTable
MakeComDimScoresTableMakeComDimScoresTable
Metadata for the lipid profiles of cell extractsmetadata_lipids
Metadata for the RNAseq data of cell extractsmetadata_RNAseq3
miRNAseq data on cell differentiationmirnaseq
MultiAssayExperiment2MultiBlockMultiAssayExperiment2MultiBlock
MultiBlockMultiBlock
MultiBlock2MatrixMultiBlock2Matrix
MultiBlock2MultiAssayExperimentMultiBlock2MultiAssayExperiment
NAInfRemoveMultiBlockNAInfRemoveMultiBlock
ncol for MultiBlockncol,MultiBlock-method
NormalizeMultiBlockNormalizeMultiBlock
nrow for MultiBlocknrow,MultiBlock-method
OPLS_NIPALS_DNROPLS_NIPALS_DNR
PredictMultiBlockPredictMultiBlock
ProcessMultiBlockProcessMultiBlock
RNAseq data on cell differentiationrnaseq
RNAseq data of cell extractsRNAseq3
sampleNamessampleNames sampleNames,MultiBlock-method
sampleNames<-sampleNames<- sampleNames<-,MultiBlock-method
SelectFeaturesRWSelectFeaturesRW
SimulateMultiBlockSimulateMultiBlock
SplitRWSplitRW
SummarizedExperiment2MultiBlockSummarizedExperiment2MultiBlock
variableNamesvariableNames variableNames,MultiBlock-method
variableNames<-variableNames<- variableNames<-,MultiBlock-method