Description Usage Arguments Value Author(s) See Also Examples

All parameters is saved to metadata slot of SingleCellExperiment object.

1 2 3 4 5 | ```
cellCellDecomp(sce, algorithm=c("ntd2", "ntd", "nmf", "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, verbose=FALSE,
centering=TRUE, mergeas=c("mean", "sum"), outerfunc=c("*", "+"),
comb=c("random", "all"), num.sampling=100, num.perm=1000, assayNames = "counts", decomp=TRUE)
``` |

`sce` |
The object generated by instantization of SingleCellExperiment-class. |

`algorithm` |
Algorithm for constrcting cell-cell similarity matrix. "ntd2", "ntd", "nmf", "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). |

`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). |

The result is saved to metadata slot of SingleCellExperiment object.

Koki Tsuyuzaki

1 | ```
showMethods("cellCellDecomp")
``` |

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