dot-singleThreadOfPhysioCalc: Mapping one sample into a physiological-space

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

Description

.singleThreadOfPhysioCalc is an internal function of calculatePhysioMap, computing the main mapping. We don't recommend the use of .singleThreadOfPhysioCalc outside of calculatePhysioMap().

Usage

.singleThreadOfPhysioCalc(
  SampleNum,
  InputData,
  Space,
  GenesRatio,
  NGenes,
  STATICResponse,
  pb,
  TTEST
)

Arguments

SampleNum	A sample (column) number of InputData.
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'.
GenesRatio	The ratio of gene expression values to be considered in the calculation. In high dimensional omics data, signal to noise ratio has a direct relation with the relative magnitude of expressions. We aim to remove the noisy genes, hence we only keep the "GenesRatio*100" percent highest and lowest gene expression values of each sample. GenesRatio should be a numerical value between 0 and 1. Default value is 0.05.
NGenes	Number of genes (rows) in Space.
STATICResponse	Logical value indicating if 'statistic' should be returned rather than the default 'signed p value'. Default value is FALSE.
pb	Progress bar made by progress::progress_bar$new.
TTEST	Logical value indicating if t.test should be done in place of the default wilcoxon rank-sum test (more info can be found in the original PhysioSpace: Lenz et. al., PLOS One 2013). Using t.test will speed up calculations. Default value is FALSE.

Value

Vector of mapped 'InputData[,SampleNum]' values in 'Space'. Mapped values are signed p value when STATICResponse==FALSE, and are 'statistic' value when STATICResponse==TRUE (more info can be found in the original PhysioSpace: Lenz et. al., PLOS One 2013).

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