RawDataGetters: Raw data 'COTAN' accessors

In seriph78/COTAN: COexpression Tables ANalysis

Raw data COTAN accessors

Description

These methods extract information out of a just created COTAN object. The accessors have read-only access to the object.

Usage

## S4 method for signature 'COTAN'
getRawData(objCOTAN)

## S4 method for signature 'COTAN'
getNumCells(objCOTAN)

## S4 method for signature 'COTAN'
getNumGenes(objCOTAN)

## S4 method for signature 'COTAN'
getCells(objCOTAN)

## S4 method for signature 'COTAN'
getGenes(objCOTAN)

## S4 method for signature 'COTAN'
getZeroOneProj(objCOTAN)

## S4 method for signature 'COTAN'
getCellsSize(objCOTAN)

## S4 method for signature 'COTAN'
getNumExpressedGenes(objCOTAN)

## S4 method for signature 'COTAN'
getGenesSize(objCOTAN)

## S4 method for signature 'COTAN'
getNumOfExpressingCells(objCOTAN)

Arguments

objCOTAN

a COTAN object

Details

getRawData() extracts the raw count table.

getNumCells() extracts the number of cells in the sample (m)

getNumGenes() extracts the number of genes in the sample (n)

getCells() extract all cells in the dataset.

getGenes() extract all genes in the dataset.

getZeroOneProj() extracts the raw count table where any positive number has been replaced with 1

getCellsSize() extracts the cell raw library size.

getNumExpressedGenes() extracts the number of genes expressed for each cell. Exploits a feature of Matrix::CsparseMatrix

getGenesSize() extracts the genes raw library size.

getNumOfExpressingCells() extracts, for each gene, the number of cells that are expressing it. Exploits a feature of Matrix::CsparseMatrix

Value

getRawData() returns the raw count sparse matrix

getNumCells() returns the number of cells in the sample (m)

getNumGenes() returns the number of genes in the sample (n)

getCells() returns a character array with the cells' names

getGenes() returns a character array with the genes' names

getZeroOneProj() returns the raw count matrix projected to 0 or 1

getCellsSize() returns an array with the library sizes

getNumExpressedGenes() returns an array with the library sizes

getGenesSize() returns an array with the library sizes

getNumOfExpressingCells() returns an array with the library sizes

Examples

data("test.dataset")
objCOTAN <- COTAN(raw = test.dataset)

rawData <- getRawData(objCOTAN)

numCells <- getNumCells(objCOTAN)

numGenes <- getNumGenes(objCOTAN)

cellsNames <- getCells(objCOTAN)

genesNames <- getGenes(objCOTAN)

zeroOne <- getZeroOneProj(objCOTAN)

cellsSize <- getCellsSize(objCOTAN)

numExpGenes <- getNumExpressedGenes(objCOTAN)

genesSize <- getGenesSize(objCOTAN)

numExpCells <- getNumOfExpressingCells(objCOTAN)

seriph78/COTAN documentation built on Nov. 15, 2024, 7:09 a.m.