setters: setters

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

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

setSuggestedClustersNumber(theObject) <- value

setCellsSimilarityMatrix(theObject) <- value

setClustersSimilarityMatrix(theObject) <- value

setClustersSimiliratyOrdered(theObject) <- value

setMarkerGenesList(theObject) <- value

setTopMarkers(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).

setSuggestedClustersNumber: Update the suggestedClustersNumber slot.

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).

setTopMarkers: Update the topMarkers 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"

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