saveBiomarkerRes: saveBiomarkerRes Save biomarker gene information with a...

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

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)

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.