cellCellDecomp: Performing scTensor

Description Usage Arguments Value Author(s) See Also Examples

Description

All parameters is saved to metadata slot of SingleCellExperiment object.

Usage

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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).

Value

The result is saved to metadata slot of SingleCellExperiment object.

Author(s)

Koki Tsuyuzaki

See Also

SingleCellExperiment.

Examples

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showMethods("cellCellDecomp")

rikenbit/scTensor documentation built on Dec. 16, 2021, 5:51 p.m.