cellCellRanks {scTensor} | R Documentation

## Rank estimation of the CCI-tensor

### Description

SVD is performed in each mode.

### Usage

    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=0.9)

### Arguments

`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: 0.9 (0 to 1)).

### Value

A vector with three elements, in which each element means the estimated ranks in mode-1, 2 and 3 matricization.

### Author(s)

Koki Tsuyuzaki

### See Also

`SingleCellExperiment`.

### Examples

    showMethods("cellCellRanks")

[Package scTensor version 1.0.13 Index]