cellCellDecomp: Performing scTensor
In rikenbit/scTensor: Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

cellCellDecomp

R Documentation

Performing scTensor

Description

All parameters is saved to metadata slot of SingleCellExperiment object.

Usage

cellCellDecomp(sce, algorithm=c("ntd2", "ntd", "nmf", "cx", "pearson",
    "spearman", "distance", "pearson.lr", "spearman.lr", "distance.lr",
    "pcomb", "label.permutation", "cabello.aguilar", "halpern"), ranks=c(3,3), rank=3, thr1=log2(5), thr2=25, thr3=0.95, L1_A=0, L2_A=0, verbose=FALSE,
    centering=TRUE, mergeas=c("mean", "sum"), outerfunc=c("*", "+"),
    comb=c("random", "all"), num.sampling=100, num.perm=1000, assayNames = "counts", decomp=TRUE)

Arguments

`sce`	The object generated by instantization of SingleCellExperiment-class.
`algorithm`	Algorithm for constrcting cell-cell similarity matrix. "ntd2", "ntd", "nmf", "cx", "pearson", "spearman", "distance", "pearson.lr", "spearman.lr", "distance.lr", "pcomb" or "label.permutation" can be specified (Default: ntd2).
`ranks`	The size of the core tensor decomposed by NTD. Each element means (Number of Ligand-Cell Pattern, Number of Receptor-Cell Pattern, Number of LR-pairs Pattern) (Default: c(3,3)).
`rank`	The number of low dimension of NMF (Default: 3).
`thr1`	The threshold used by pcomb (Default: log2(5)).
`thr2`	The threshold used by pcomb (Default: 25).
`thr3`	The threshold used by cx (Default: 0.95).
`L1_A`	The parameter to control the sparseness (Default: 0).
`L2_A`	The parameter to control the outlier (Default: 0).
`verbose`	The verbose parameter for nnTensor::NTD (Default: FALSE).
`centering`	When the value is TRUE, input matrix is summarized as celltype-level vectors (Default: TRUE).
`mergeas`	When the centering is TRUE, "sum" (celltype-level sum vector) or "mean" (celltype-level average vector) is calculated (Default: "sum").
`outerfunc`	When the centering is TRUE, "+" (Kronecker sum) or "*" (Kronecker product) 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").
`decomp`	When the value is TRUE, cell-cell interaction tensor is decomposed (Default: TRUE).