getCiceroGeneActivities-methods

Obtain Cicero gene activities

# S4 method for DsATAC
getCiceroGeneActivities(
  .object,
  regionType,
  promoterGr = NULL,
  maxDist = 250000L,
  corCutOff = 0.35,
  dimRedCoord = NULL,
  knn.k = 50
)

Arguments

.object

DsATAC object

regionType

region type of regions that will be linked to the promoter (typical some sort of peak annotation)

promoterGr

GRanges object of promoter coordinates

maxDist

maximum distance to consider for region-region interactions

corCutOff

cutoff of correlation coefficients (Pearson) to consider for region-region interactions

dimRedCoord

matrix of reduced dimension coordinates. must have coordinates for all samples/cells in the dataset

knn.k

parameter k for Cicero's k-nearest-neighbor method

Value

an SummarizedExperiment object containing gene activities for all cells/samples in the dataset

Author

Fabian Mueller