R/runBatchCorrection.R
runSCANORAMA.Rd
SCANORAMA is analogous to computer vision algorithms for panorama stitching that identify images with overlapping content and merge these into a larger panorama.
runSCANORAMA( inSCE, useAssay = "logcounts", batch = "batch", SIGMA = 15, ALPHA = 0.1, KNN = 20L, assayName = "SCANORAMA" )
inSCE | SingleCellExperiment inherited object. Required. |
---|---|
useAssay | A single character indicating the name of the assay requiring
batch correction. Scanorama requires a transformed normalized expression
assay. Default |
batch | A single character indicating a field in
|
SIGMA | A numeric scalar. Algorithmic parameter, correction smoothing
parameter on Gaussian kernel. Default |
ALPHA | A numeric scalar. Algorithmic parameter, alignment score
minimum cutoff. Default |
KNN | An integer. Algorithmic parameter, number of nearest neighbors to
use for matching. Default |
assayName | A single characeter. The name for the corrected assay. Will
be saved to |
The input SingleCellExperiment object with
assay(inSCE, assayName)
updated.
Brian Hie et al, 2019
if (FALSE) { data('sceBatches', package = 'singleCellTK') sceBatches <- scaterlogNormCounts(sceBatches) sceCorr <- runSCANORAMA(sceBatches, "ScaterLogNormCounts") }