getCiceroGeneActivities,DsATAC-method | R Documentation |
Obtain Cicero gene activities
## S4 method for signature 'DsATAC'
getCiceroGeneActivities(
.object,
regionType,
promoterGr = NULL,
maxDist = 250000L,
corCutOff = 0.35,
dimRedCoord = NULL,
knn.k = 50
)
.object |
|
regionType |
region type of regions that will be linked to the promoter (typical some sort of peak annotation) |
promoterGr |
|
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 |
an SummarizedExperiment
object containing gene activities for all cells/samples in the dataset
Fabian Mueller
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