7.2 Clustering using scran

Additionally, ArchR allows for the identification of clusters with scran by changing the method parameter in addClusters().

projHeme2 <- addClusters(
    input = projHeme2,
    reducedDims = "IterativeLSI",
    method = "scran",
    name = "ScranClusters",
    k = 15
)
## ArchR logging to : ArchRLogs/ArchR-addClusters-371b038d9b170-Date-2022-12-23_Time-06-09-53.log
## If there is an issue, please report to github with logFile!
## 2022-12-23 06:09:54 : Running Scran SNN Graph (Lun et al. F1000Res. 2016), 0.001 mins elapsed.
## 2022-12-23 06:09:56 : Identifying Clusters (Lun et al. F1000Res. 2016), 0.03 mins elapsed.
## 2022-12-23 06:13:30 : Testing Outlier Clusters, 3.602 mins elapsed.
## 2022-12-23 06:13:30 : Assigning Cluster Names to 10 Clusters, 3.602 mins elapsed.
## 2022-12-23 06:13:30 : Finished addClusters, 3.603 mins elapsed.