export2loom: export2loom

In aertslab/SCENIC: SCENIC (Single Cell rEgulatory Network Inference and Clustering)

export2loom

Description

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

Usage

export2loom(
  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

# devtools::install_github("aertslab/SCopeLoomR")
# scenicOptions@fileNames$output["loomFile",] <- "myAnalysis.loom"
# export2scope(scenicOptions, exprMat, hierarchy=c("SCENIC", "MouseBrain"))

aertslab/SCENIC documentation built on April 7, 2024, 10 a.m.