exportResults-scRNAseq: exportResults

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

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)

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