exportResults,scRNAseq-method {conclus} | R Documentation

## exportResults

### Description

Export all the results of Conclus to a Results sub-directory.

### Usage

    exportResults(theObject, saveClusteringResults=TRUE, saveAll=FALSE,
    saveNormalizedMatrix=FALSE, saveColData=FALSE, saveRowData=FALSE,
    saveTsne=FALSE, saveDBScan=FALSE, saveCellsSimilarityMatrix=FALSE,
    saveClustersSimilarityMatrix=FALSE, saveFullMarkers=FALSE,
    saveTopMarkers=FALSE, saveGenesInfos=FALSE)

### Arguments

`theObject` | An Object of class scRNASeq for which different steps of CONCLUS was applied to. The number of steps to run depends on what is wanted to be saved.
`saveClusteringResults` | Default=TRUE. Save the final clustering results giving the corresponding cluster number to each cell. The method ?calculateClustersSimilarity should have been run on the object. It is saved in the sub-directory 6_ConclusResult.
`saveAll` | Default=FALSE. Save all results of CONCLUS. The last step run on the scRNASeq object should be ?retrieveGenesInfo.
`saveNormalizedMatrix` | Default=FALSE. Save the normalized count matrix as a csv file. It is obtained with ?normaliseCountMatrix. The matrix is saved to the sub-directory '1_MatrixInfo'.
`saveColData` | Default=FALSE. Save the columns metadata of the normalized count matrix as a tsv file. These data are obtained with ?normaliseCountMatrix or were given as input of the method. These data are saved in the sub-directory '1_MatrixInfo'.
`saveRowData` | Default=FALSE. Save the raw metadata of the normalized count matrix as a tsv file. These data are obtained with ?normaliseCountMatrix. They are saved in the sub-directory '1_MatrixInfo'.
`saveTsne` | Default=FALSE. Save the tsne coordinates for each combination of PCs and perplexities as tsv files. These coordinates were obtained with ?generateTSNECoordinates. They are saved in the sub-directory '2_TSNECoordinates'.
`saveDBScan` | Default=FALSE. Save the clustering results of dbscan as tsv files. The number of clustering solutions is PCs*perplexity*epsilon*minPoints (see ?runDBSCAN, 84 solutions by default). These are saved in the sub-directory '3_dbScan'.
`saveCellsSimilarityMatrix` | Default=FALSE. Save the cells similarity matrix that was obtained with ?clusterCellsInternal. This matrix is saved in the sub-directory '4_CellSimilarityMatrix'.
`saveClustersSimilarityMatrix` | Default=FALSE. Save the cluster similarity matrix that was obtained with ?calculateClustersSimilarity. It is saved in the sub-directory '5_ClusterSimilarityMatrix'.
`saveFullMarkers` | Default=FALSE. Save the lists of markers that were obtained with ?rankGenes to the sub-directory 7_fullMarkers.
`saveTopMarkers` | Default=FALSE. Save the top markers per clusters as csv files in the sub-directory '8_TopMarkers'. See ?retrieveTopClustersMarkers for more details.
`saveGenesInfos` | Default=FALSE. Save the genes information for each cluster as csv files in the sub-directory '9_genesInfos'. See ?retrieveGenesInfo for more details.

### Value

Sub-directories containing the results of the different conclus steps. See the 'Quick start' section of the vignette for details.

### Author(s)

Ilyess RACHEDI and Nicolas DESCOSTES.

### Examples

    ## Object scr containing the results of previous steps
    load(system.file("extdata/scrFull.Rdat", package="conclus"))

    ## Saving all results
    exportResults(scr, saveAll=TRUE)

    ## Removing output directory
    unlink("YourOutputDirectory", recursive=TRUE)

[Package conclus version 1.0.0 Index]