dot-inptPreparer: Preparing InputData for Calculation

In JRC-COMBINE/PhysioSpaceMethods: Creates and uses physio spaces as a dimension reduction mapping

Description

.inptPreparer is an internal function used by .inptChecker and spaceMaker to set up row and column names of 'InputData', and convert it to a matrix, if necessary.

Usage

.inptPreparer(InputData)

Arguments

InputData

A matrix, SummarizedExperiment object or a list, based on the gene expression data (or any other type of high dimensional data, e.g. protein abundance, SNP, Methylation, etc.), to be analysed. InputData has to have a specific format to be properly analysed, these requirements are thoroughly explained in the 'Details' section of calculatePhysioMap() function.

Value

.inptPreparer returns InputData as a matrix with proper row and column names.

Examples

## Not run: 
 SimulatedGeneExpressionData <- matrix(
   rnorm(n = 100000, mean = 0,
         sd = 100),
   ncol = 10,
   dimnames = list(1:10000, 1:10)
 )
 SimulatedGeneExpressionData_checked <-
     PhysioSpaceMethods:::.inptPreparer(SimulatedGeneExpressionData)

 library(SummarizedExperiment)
 SimulatedGeneExpressionData_SE <- SummarizedExperiment(
     assays = list(GEX = SimulatedGeneExpressionData),
     rowData = data.frame("EntrezID" =
                              rownames(SimulatedGeneExpressionData)),
     colData = data.frame("SampleName" =
                              colnames(SimulatedGeneExpressionData))
 )
 SimulatedGeneExpressionData_SE_checked <-
     PhysioSpaceMethods:::.inptPreparer(SimulatedGeneExpressionData_SE)

## End(Not run)

JRC-COMBINE/PhysioSpaceMethods documentation built on July 27, 2021, 12:53 p.m.