cellCellReport {scTensor} | R Documentation

## HTML report of the result of scTensor

### Description

The result is saved as HTML report which contains with multiple files.

### Usage

    cellCellReport(sce, reducedDimNames,
        out.dir=tempdir(), html.open=FALSE,
        title="The result of scTensor",
        author="The person who runs this script", assayNames = "counts", thr=100,
        top="full", p=0.05, upper=20,
        goenrich=TRUE, meshenrich=TRUE, reactomeenrich=TRUE,
        doenrich=TRUE, ncgenrich=TRUE, dgnenrich=TRUE, nbins=40)

### Arguments

`sce` | A object generated by instantization of SingleCellExperiment-class.
`reducedDimNames` | The name of two-dimentional data saved in reducedDimNames slot of SingleCellExperiment object.
`out.dir` | The output directory for saving HTML report (out.dir: tempdir()).
`html.open` | Whether the result of HTML report is opened when the calculation is finished (Default: FALSE).
`title` | The title of HTML report (Default: "The result of scTensor").
`author` | The author of HTML report (Default: "The person who runs this script").
`assayNames` | The unit of gene expression for using scTensor (e.g. normcounts, cpm...etc) (Default: "counts").
`thr` | The threshold for selection of top pecentage of core tensor elements (Default: 100 (1 to 100)).
`top` | top genes in each (*,*,*)-pattern which are selected and summarized in the report (Default: "full")
`p` | The threshold of p-value of the enrichment analysis (Default: 1E-2)
`upper` | The maxium number of HTML reports generates (Default: 20)
`goenrich` | Whether GO-Enrichment analysis is performed (Default: TRUE)
`meshenrich` | Whether MeSH-Enrichment analysis is performed (Default: TRUE)
`reactomeenrich` | Whether Reactome-Enrichment analysis is performed (Default: TRUE)
`doenrich` | Whether DO-Enrichment analysis is performed (Default: TRUE)
`ncgenrich` | Whether NCG-Enrichment analysis is performed (Default: TRUE)
`dgnenrich` | Whether DGN-Enrichment analysis is performed (Default: TRUE)
`nbins` | The number of bins used for the two dimensional plot of schex (Default: 40)

### Value

The result is saved as HTML report which contains with multiple files.

### Author(s)

Koki Tsuyuzaki

### See Also

`SingleCellExperiment`.

### Examples

    	if(interactive()){
    	# Package Loading
    	library("SingleCellExperiment")
    	library("AnnotationHub")
    	if(!require(LRBaseDbi)){
    	    BiocManager::install("LRBaseDbi")
    	    library(LRBaseDbi)
    	}
    	ah <- AnnotationHub()
    	dbfile <- query(ah, c("LRBaseDb", "Homo sapiens", "v002"))[[1]]
    	LRBase.Hsa.eg.db <- LRBaseDbi::LRBaseDb(dbfile)

    	# Data Loading
    	data(GermMale)
    	data(labelGermMale)
    	data(tsneGermMale)

    	# SingleCellExperiment Object
    	sce <- SingleCellExperiment(assays=list(counts = GermMale))
    	reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y)

    	# User's Original Normalization Function
    	CPMED <- function(input){
    	    libsize <- colSums(input)
    	    median(libsize) * t(t(input) / libsize)
    	}
    	# Normalization
    	normcounts(sce) <- log10(CPMED(counts(sce)) + 1)

    	# Registration of required information into metadata(sce)
    	cellCellSetting(sce, LRBase.Hsa.eg.db, names(labelGermMale))

    	# Rank Estimation
    	rks <- cellCellRanks(sce, assayNames="normcounts")

    	# CCI Tensor Decomposition
    	set.seed(1234)
    	cellCellDecomp(sce, ranks=rks$selected, assayNames="normcounts")

    	# HTML Report
    	options(device.ask.default = FALSE)
    	cellCellReport(sce, reducedDimNames="TSNE",
            out.dir=tempdir(), html.open=FALSE,
            title="The result of scTensor",
            author="The person who runs this script",
            assayNames="counts", thr=100,
            top="full", p=0.05, upper=20,
            goenrich=TRUE, meshenrich=TRUE, reactomeenrich=TRUE,
            doenrich=TRUE, ncgenrich=TRUE, dgnenrich=TRUE, nbins=40)
        }else{
            showMethods("cellCellReport")
        }

[Package scTensor version 2.4.1 Index]