setters {conclus} | R Documentation

## setters

### Description

Update a slot of a scRNA-seq, Tsne or Dbscan object.

### Usage

    setExperimentName(theObject) <- value

    setCountMatrix(theObject) <- value

    setSceNorm(theObject) <- value

    setSpecies(theObject) <- value

    setOutputDirectory(theObject) <- value

    setTSNEList(theObject) <- value

    setDbscanList(theObject) <- value

    setCellsSimilarityMatrix(theObject) <- value

    setClustersSimilarityMatrix(theObject) <- value

    setClustersSimiliratyOrdered(theObject) <- value

    setMarkerGenesList(theObject) <- value

    setClustersMarkers(theObject) <- value

    setGenesInfos(theObject) <- value

    ## S4 replacement method for signature 'Tsne'
    setName(theObject) <- value

    setPC(theObject) <- value

    setPerplexity(theObject) <- value

    setCoordinates(theObject) <- value

    setName(theObject) <- value

    setEpsilon(theObject) <- value

    setMinPoints(theObject) <- value

    setClustering(theObject) <- value

### Arguments

`theObject` | A scRNA-seq, Tsne or Dbscan object to update. See description or ?scRNAseq, ?Tsne or ?Dbscan.
`value` | The value to update the slot with. See ?scRNAseq, ?Tsne or ?Dbscan.

### Value

setExperimentName: Update the experiment name slot with a character string (scRNA-seq).

setCountMatrix: Update the countMatrix slot with a matrix of numeric (scRNA-seq).

setSceNorm: Update the normalized countMatrix slot with SingleCellExperiment object (scRNA-seq).

setSpecies: Update the species slot with a character string. Value should be mouse or human. Other organisms can be added on demand (scRNA-seq).

setOutputDirectory: Update the outputDirectory slot with a character string. Value should be a valid path (scRNA-seq).

setTSNEList: Update the tSNEList slot with a list of tSNE objects. See ?Tsne-class (scRNA-seq).

setDbscanList: Update the dbscanList slot with a list of dbscan objects. See ?Dbscan-class (scRNA-seq).

setCellsSimilarityMatrix: Update the cellsSimilarityMatrix slot with a numeric matrix (scRNA-seq).

setClustersSimilarityMatrix: Update the clustersSimilarityMatrix slot with a numeric matrix (scRNA-seq).

setClustersSimiliratyOrdered: Update the clustersSimilarityOrdered slot with a numeric factor (scRNA-seq).

setMarkerGenesList: Update the markerGenesList slot with a list of data frame. The data frame structure should be: data.frame(Gene = c("gene1"), mean_log10_fdr = c(NA), n_05 = c(NA), score = c(NA)) (scRNA-seq).

setClustersMarkers: Update the clustersMarkers slot with a data frame. The data frame structure should be: data.frame(geneName="gene1", clusters=NA). (scRNA-seq)

setGenesInfos: Update the genesInfos slot with a data frame. The data frame structure should be: data.frame(uniprot_gn_symbol=c("symbol"), clusters="1", external_gene_name="gene", go_id="GO1,GO2", mgi_description="description", entrezgene_description="descr", gene_biotype="gene", chromosome_name="1", Symbol="symbol", ensembl_gene_id="ENS", mgi_id="MGI", entrezgene_id="1", uniprot_gn_id="ID"). (scRNA-seq)

setPC: Update the pc slot with a vector of numeric (Tsne).

setPerplexity: Update the perplexity slot with a vector of numeric (Tsne).

setCoordinates: Update the coordinates slot with a matrix of numeric (Tsne).

setName: Update the Tsne or Dbscan name slot with a character string (Dbscan).

setEpsilon: Update the epsilon slot with a vector of numeric (Dbscan).

setMinPoints: Update the minPoints slot with a vector of numeric (Dbscan).

setClustering: Update the clustering slot with a matrix of numeric (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")

    setExperimentName(scr) <- "newName"
    setCountMatrix(scr) <- countMatrix[seq_len(10), seq_len(10)]
    setSpecies(scr) <- "human"
    setOutputDirectory(scr) <- "newPath"

[Package conclus version 1.0.0 Index]