dot-inptChecker: Checking calculatePhysioMap Inputs

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

Description

.inptChecker is an internal function used by calculatePhysioMap for checking the format of inputs, 'InputData' and 'Space' to be exact. It 1- checks to see if both 'InputData' and 'Space' are matrices, and 2- matches the rows of 'InputData' or 'Space' based on their row names.

Usage

.inptChecker(InputData, Space)

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.
Space	The space in which the 'InputData' will be mapped. Just as 'InputData', it should be a matrix with genes as rows and samples as columns, with corresponding Entrez Gene IDs in 'rownames' of the matrix, and name of each axis of the space written in 'colnames'.

Value

.inptChecker returns corrected 'InputData' and 'Space' directly to the environment it was called from (By assigning new matrices to parent.frame()).

Examples

## Not run: 
 SimulatedGeneExpressionData <-
   matrix(
     rnorm(n = 100000, mean = 0, sd = 100),
     ncol = 10,
     dimnames = list(1:10000, 1:10)
   )
 PhysioSpaceMethods:::.inptChecker(InputData =
                                         SimulatedGeneExpressionData[, 1:5],
              Space = SimulatedGeneExpressionData[sample(1:10000), 6:10])

## End(Not run)

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