makePartialLeastSquaresRegression: Calculate PLS on data returned from decoration methods.

In cmujzbit/OmicsON: OmicsON is a package implementing workflow for finding associations acrossomics data sets

Description

Function is used to easily perform PLS analysis on functional interactions data frames, those data frames are returned from OmicsON::createFunctionalInteractionsDataFrame which works directly on data returned from functions responsible for decoration. To close workflow, you can then use dedicated plotting functions on returned data, which are OmicsON::plotRmsepForPLS and OmicsON::plotRegression.

Usage

makePartialLeastSquaresRegression(xNamesVector, yNamesVector, XDataFrame,
  YDataFrame, formula = Y ~ X, ncompValue = 10, xCutoff = 1,
  yCutoff = 1, ...)

Arguments

xNamesVector	A vector of names from functional interactions data frame. Mostly genes symbols.
yNamesVector	A vector of names from functional interactions data frame. Mostly root column.
XDataFrame	A data frame with data to PLS analysis. This argument is strongly connected with xNamesVector arg.
YDataFrame	A data frame with data to PLS analysis. This argument is strongly connected with yNamesVector arg.
formula	Formula to use in PLs, default is Y ~ X.
ncompValue	Number of components in PLS analysis.
xCutoff	You can use it to remove highly correlated variables on XDataFrame.
yCutoff	You can use it to remove highly correlated variables on YDataFrame.
...	Other arguments put into pls::plsr function, which is responsible for calculations.

Value

List with PLS results data.

Examples

ontology2GenesSymboleFromEnsembleFunctionalInteractions <- OmicsON::createFunctionalInteractionsDataFrame(
decoratedByReactome,
singleIdColumnName = 'ontologyId',
idsListColumnName = 'genesSymbolsFromEnsemble')
ccaResultsEnsemble <- OmicsON::makeCanonicalCorrelationAnalysis(
xNamesVector = ontology2GenesSymboleFromEnsembleFunctionalInteractions$genesSymbolsFromEnsemble,
yNamesVector = ontology2GenesSymboleFromEnsembleFunctionalInteractions$root,
XDataFrame = transcriptomicsInputData,
YDataFrame = lipidomicsInputData, xCutoff = 0.5, yCutoff = 0.75)

cmujzbit/OmicsON documentation built on May 12, 2020, 8:06 p.m.