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, ftt=TRUE, 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).

ftt

When the value is TRUE, Freeman-Tuckey transformation (FTT) of data matrix is calculated (Default: TRUE).

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 1.0.2 Index]