settingTGIF {scTGIF}R Documentation

Paramter setting for scTGIF

Description

All parameters is saved to metadata slot of SingleCellExperiment object.

Usage

settingTGIF(sce, gmt, reducedDimNames, assayNames="counts", grid.size=50)

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").

grid.size

The grid size for segmentation of the two dimensional plot of reducedDim(sce) (Default: 50, which means 50*50 grids).

Value

The result is saved to metadata slot of SingleCellExperiment object.

Author(s)

NA

Examples

showMethods("settingTGIF")

[Package scTGIF version 1.0.0 Index]