SCENIC (version 1.1.2-01)

export2scope: export2scope

Description

Create .loom file with the results of the analysis to visualize them in http://scope.aertslab.org

Usage

export2scope(scenicOptions, dgem, hierarchy = c("SCENIC", "", ""),
  addAllTsnes = TRUE)

Arguments

scenicOptions

scenicOptions object

dgem

Digital expression matrix

hierarchy

Labels for the hierarchy levels (up to three)

Value

The .loom file (file name indicated in "loomFile" slot in scenicOptions) containing the following information:

• dgem (digital expression matrix)

• title: getDatasetInfo(scenicOptions,"datasetTitle")

• genome: getDatasetInfo(scenicOptions,"org")

• regulons.AUC: getAUC(loadInt(scenicOptions, "aucell_regulonAUC"))

• regulons: loadInt(scenicOptions, "aucell_regulons")

• default.embedding: default t-SNE

• default.embedding.name: default t-SNE type (e.g. AUC/binary and description)

• column attributes: getDatasetInfo(scenicOptions, "cellInfo") and nGene (colSums(dgem>0)).

See Also

To add extra data (e.g. embeddings or clusters), see: help(package="SCopeLoomR")

Examples

# NOT RUN {
# devtools::install_github("aertslab/SCopeLoomR")
# scenicOptions@fileNames$output["loomFile",] <- "myAnalysis.loom"
# export2scope(scenicOptions, exprMat, hierarchy=c("SCENIC", "MouseBrain"))
# }