cellCellRanks: Rank estimation of the CCI-tensor
In rikenbit/scTensor: Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

cellCellRanks

R Documentation

Rank estimation of the CCI-tensor

Description

SVD is performed in each mode.

Usage

cellCellRanks(sce, centering=TRUE,
    mergeas=c("mean", "sum"), outerfunc=c("*", "+"), comb=c("random", "all"),
    num.sampling=100, num.perm=1000, assayNames = "counts", verbose=FALSE,
    num.iter1=5, num.iter2=5, num.iter3=NULL)

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").
`outerfunc`	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).
`num.perm`	The number of the permutation in label permutation test (Default: 1000).
`assayNames`	The unit of gene expression for using scTensor (e.g. normcounts, cpm...etc) (Default: "counts").
`verbose`	The verbose parameter for nnTensor::NTD (Default: FALSE).
`num.iter1`	The number of iteration to estimate the rank of mode-1 matricised data tensor (Default: 5).
`num.iter2`	The number of iteration to estimate the rank of mode-2 matricised data tensor (Default: 5).
`num.iter3`	The number of iteration to estimate the rank of mode-3 matricised data tensor (Default: NULL).

Value

RSS: A list with three elements, in which each element means the average reconstructed error in each rank. selected: A vector with three elements, in which each element means the estimated ranks in mode-1, 2 and 3 matricization.