Find_Markers: Find_Markers

In bimberlabinternal/OOSAP: OHSU-ONPRC Single-cell Analysis Package

Description

Find_Markers

Usage

Find_Markers(
  seuratObj,
  resolutionToUse,
  outFile = NULL,
  saveFileMarkers = NULL,
  testsToUse = c("wilcox", "bimod", "roc", "t", "negbinom", "poisson", "LR", "MAST",
    "DESeq2"),
  numGenesToSave = 20,
  onlyPos = F,
  includeNameTranslation = T
)

Arguments

seuratObj	A seurat object
resolutionToUse	The resolution, generally computed during FindClustersAndDimRedux()
outFile	A file where a table of markers will be saved
saveFileMarkers	A file where the dataframe of markers will be saved as RDS
testsToUse	A vector of tests to be used. Each will be used to run FindAllMarkers() and the results merged
numGenesToSave	The number of top markers per cluster to save
onlyPos	If true, only positive markers will be saved

bimberlabinternal/OOSAP documentation built on Jan. 19, 2021, 2:47 a.m.