cellCellRanks {scTensor} | R Documentation |
SVD is performed in each mode.
cellCellRanks(sce, centering=TRUE, mergeas=c("mean", "sum"), outer=c("*", "+"), comb=c("random", "all"), num.sampling=100, assayNames = "counts", thr1=0.9, thr2=0.9, thr3=NULL)
sce |
A object generated by instantization of SingleCellExperiment-class. |
centering |
When the value is TRUE, input matrix is summarized as celltype-level vectors (Default: TRUE). |
mergeas |
When the centering is TRUE, "mean" (celltype-level mean vector) or "sum" (celltype-level sum vector) is calculated (Default: "mean"). |
outer |
When the centering is TRUE, "*" (Kronecker product) or "+" (Kronecker sum) or is calculated (Default: "+"). |
comb |
When the centering is FALSE, "random" (random cell-cell pairing) or "all" (all possible cell-cell pairing) is calculed (Default: "random"). |
num.sampling |
The number of random sampling used (Default: 100). |
assayNames |
The unit of gene expression for using scTensor (e.g. normcounts, cpm...etc) (Default: "counts"). |
thr1 |
The threshold for selection of top eigenvalues of mode-1 matricised data tensor (Default: 0.9 (0 to 1)). |
thr2 |
The threshold for selection of top eigenvalues of mode-2 matricised data tensor (Default: 0.9 (0 to 1)). |
thr3 |
The threshold for selection of top eigenvalues of mode-3 matricised data tensor (Default: NULL (0 to 1)). |
A vector with three elements, in which each element means the estimated ranks in mode-1, 2 and 3 matricization.
Koki Tsuyuzaki
showMethods("cellCellRanks")