getters: getters

In ilyessr/conclus: ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

getters

Description

Retrieve the data of the slots of a scRNA-seq, Tsne or Dbscan object.

Usage

getExperimentName(theObject)

getCountMatrix(theObject)

getSceNorm(theObject)

getSpecies(theObject)

getOutputDirectory(theObject)

getTSNEList(theObject)

getDbscanList(theObject)

getSuggestedClustersNumber(theObject)

getCellsSimilarityMatrix(theObject)

getClustersSimilarityMatrix(theObject)

getClustersSimilarityOrdered(theObject)

getMarkerGenesList(theObject, cluster)

getTopMarkers(theObject)

getGenesInfos(theObject)

## S4 method for signature 'Tsne'
getName(theObject)

getPerplexity(theObject)

getPC(theObject)

getCoordinates(theObject)

getName(theObject)

getEpsilon(theObject)

getMinPoints(theObject)

getClustering(theObject)

Arguments

theObject	A scRNA-seq, Tsne or Dbscan object. See description or ?scRNAseq, ?Tsne, ?Dbscan.
cluster	Integer, index of the cluster to retrive the gene list. If cluster="all", get the marker list for each cluster into a list.

Value

getExperimentName: Get the name of the experiment (scRNA-seq).

getCountMatrix: Get the count matrix (scRNA-seq).

getSceNorm: Get the SingleCellExperiment object used (scRNA-seq).

getSpecies: Get the species (scRNA-seq).

getOutputDirectory: Get the path of the output directory (scRNA-seq).

getTSNEList: Get the list of Tsne objects (scRNA-seq).

getDbscanList: Get the list of Dbscan objects (scRNA-seq).

getSuggestedClustersNumber: Get the suggested clusters number (scRNA-seq).

getCellsSimilarityMatrix: Get the cell similarity matrix (scRNA-seq).

getClustersSimilarityMatrix: Get the cluster similarity matrix (scRNA-seq).

getClustersSimilarityOrdered: Get the clusters ordered by similarity (scRNA-seq).

getMarkerGenesList: Get the list of marker genes by clusters (scRNA-seq).

getTopMarkers: Get the most significant markers by clusters (scRNA-seq).

getGenesInfos: Get informations about marker genes (scRNA-seq).

getPerplexity: Get the perplexity used (Tsne).

getPC: Get the PC used (Tsne).

getCoordinates: Get the matrix of tSNE coordinates (Tsne).

getName: Get the name of the tSNE or Dbscan object (Dbscan).

getEpsilon: Get the epsilon used (Dbscan).

getMinPoints: Get the MinPoint used (Dbscan).

getClustering: Get the matrix of DBSCAN clustering (Dbscan).

Author(s)

Ilyess RACHEDI

Examples

## Load the count matrix
countMatrixPath <- system.file("extdata/countMatrix.tsv", package="conclus")
countMatrix <- loadDataOrMatrix(file=countMatrixPath, type="countMatrix",
                                ignoreCellNumber=TRUE)

## Load the coldata
coldataPath <- system.file("extdata/colData.tsv", package="conclus")
columnsMetaData <- loadDataOrMatrix(file=coldataPath, type="coldata",
                                    columnID="cell_ID")

## Create the initial object
scr <- singlecellRNAseq(experimentName = "Bergiers",
                countMatrix     = countMatrix,
                species         = "mouse",
                outputDirectory = "YourOutputDirectory")

experimentName <- getExperimentName(scr)
countMatrix <- getCountMatrix(scr)
species <- getSpecies(scr)
outputDirectory <- getOutputDirectory(scr)

ilyessr/conclus documentation built on April 8, 2022, 1:43 p.m.