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 1.1.0 Index]