settingTGIF: Paramter setting for scTGIF

In scTGIF: Cell type annotation for unannotated single-cell RNA-Seq data

Description

All parameters is saved to metadata slot of SingleCellExperiment object.

Usage

settingTGIF(sce, gmt, reducedDimNames, assayNames="counts", nbins=40)

Arguments

sce	A object generated by instantization of SingleCellExperiment-class.
gmt	Object generated from GSEABase::getGmt function. GMT file can be downloaded from MSigDB web (site http://software.broadinstitute.org/gsea/login.jsp#msigdb). Please confirm that the gmt file contains Human Entrez Gene ID, not gene symbol. Also confirm that the DataMatrix has Human Entrez Gene ID.
reducedDimNames	The names of reducedDim(sce) that user want use in scTGIF.
assayNames	The unit of gene expression for using scTGIF (e.g. normcounts, cpm...etc) (Default: "counts").
nbins	The number of bins of schex (Default: 40).

Value

The result is saved to metadata slot of SingleCellExperiment object.

Author(s)

Koki Tsuyuzaki [aut, cre]

Examples

showMethods("settingTGIF")

scTGIF documentation built on Nov. 8, 2020, 5:24 p.m.