cellCellSetting: Parameter setting for scTensor

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

Parameter setting for scTensor

Description

All parameters is saved to metadata slot of SingleCellExperiment object.

Usage

cellCellSetting(sce, lrbase, label, lr.evidence="known", color=NULL)

Arguments

sce	A object generated by instantization of SingleCellExperiment-class.
lrbase	Ligand-Receptor database (LRBase.XXX.eg.db-type package).
label	Cellular label information for distingusishing which cells belong to common celltypes.
lr.evidence	The evidence code for L-R pair list (Default: "known"). When you specify "known", DLRP, IUPHAR, HPMR, CELLPHONEDB, SINGLECELLSIGNALR are searched, and other databases are searched, when you specify "putative". You can also specify multiple databases at once (e.g. c("SWISSPROT_STRING", "TREMBL_STRING")). cf. https://github.com/rikenbit/lrbase-workflow
color	Color scheme for adding color against the cells (Default: NULL). If the value is not specified, automatically the color vector is generated.

Value

The result is saved to metadata slot of SingleCellExperiment object.

Author(s)

Koki Tsuyuzaki

See Also

SingleCellExperiment.

Examples

showMethods("cellCellSetting")

rikenbit/scTensor documentation built on Jan. 28, 2023, noon