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Calculate AUC scores (akin to AUCell)

aucell_sc.Rd

Calculates an AUC-type score akin to AUCell across the gene sets, see Aibar et al. You have the options to calculate the AUC. Two options here: calculate this with proper AUROC calculations (useful for marker gene expression, use the "auroc" version) or based on the Mann-Whitney statistic (useful for pathway activity measurs, use the "wilcox"). Data can be streamed in chunks of 50k cells per or loaded in in one go.

Usage

aucell_sc(
  object,
  gs_list,
  auc_type = c("wilcox", "auroc"),
  streaming = FALSE,
  .verbose = TRUE
)

Arguments

object

SingleCells class.

gs_list

Named list. The elements have the gene identifiers of the respective gene sets.

auc_type

String. Which type of AUC to calculate. Choice of c("wilcox", "auroc").

streaming

Boolean. Shall the cell data be streamed in. Useful for larger data sets.

.verbose

Boolean. Controls the verbosity of the function.

Value

AUCell results in form of a matrix that is cells x gene sets.

References

Aibar, et al., Nat Methods, 2017