getClusterInputData {singleCellTK} | R Documentation |
Get data to use as input clustering algorithms
getClusterInputData(inSCE, inputData, useAssay = "logcounts", reducedDimName = NULL)
inSCE |
Input SCtkExperiment object. Required |
inputData |
A string ("Raw Data", "PCA Components", "tSNE Components", "UMAP Components") |
useAssay |
Indicate which assay to use for PCA. Default is "logcounts" |
reducedDimName |
If clustering on PCA, t-SNE or UMAP data, dimension name. The toolkit will store data with the pattern <ASSAY>_<ALGORITHM>. |
Cluster input data
data("mouseBrainSubsetSCE") getClusterInputData(mouseBrainSubsetSCE, "PCA Components", useAssay = "logcounts", reducedDimName = "PCA_logcounts")