saveBiomarkerRes {singleCellTK} | R Documentation

## saveBiomarkerRes Save biomarker gene information with a custom name when provided with diffex results.

### Description

saveBiomarkerRes Save biomarker gene information with a custom name when provided with diffex results.

### Usage

    saveBiomarkerRes(inSCE, diffex, biomarkerName, method, ntop = 25,
      logFC = NULL, pVal = NULL)

### Arguments

`inSCE` | Input SCtkExperiment object. Required
`diffex` | results table saved from the differential expression analysis. Required.
`biomarkerName` | name of the biomarker result to be saved under in rowData(). Required.
`method` | name of the diffex method used to generate the results. Options are DESeq2, Limma and ANOVA. Required
`ntop` | number of top N genes. Default is 25. Required
`logFC` | logfold-change cutoff applied to save biomarker results. Optional
`pVal` | adjusted p-value cutoff. Optional

### Value

a new SCE object with the diffex result saved in the rowData using the "biomarkerName"

### Examples

    data("mouseBrainSubsetSCE")
    res <- scDiffEx(mouseBrainSubsetSCE,
                    useAssay = "logcounts",
                    condition = "level1class",
                    ntop = length(rownames(mouseBrainSubsetSCE)),
                    usesig = FALSE,
                    diffexmethod = "limma")
    sceObj <- saveDiffExResults(mouseBrainSubsetSCE, res, "Limma_Level1class", "limma")
    bioMarkRes <- saveBiomarkerRes(sceObj, res, "bioMarker", "limma", logFC = 4, pVal = 0.05)

[Package singleCellTK version 1.4.2 Index]