seuratFindMarkers {singleCellTK} | R Documentation

## seuratFindMarkers

### Description

seuratFindMarkers

### Usage

    seuratFindMarkers(
      inSCE,
      cells1 = NULL,
      cells2 = NULL,
      group1 = NULL,
      group2 = NULL,
      allGroup = NULL,
      conserved = FALSE,
      test = "wilcox",
      onlyPos = FALSE,
      minPCT = 0.1,
      threshUse = 0.25,
      verbose = TRUE
    )

### Arguments

`inSCE` | Input `SingleCellExperiment` object.
`cells1` | A `list` of sample names included in group1.
`cells2` | A `list` of sample names included in group2.
`group1` | Name of group1.
`group2` | Name of group2.
`allGroup` | Name of all groups.
`conserved` | Logical value indicating if markers conserved between two groups should be identified. Default is `FALSE`.
`test` | Test to use for DE. Default `"wilcox"`.
`onlyPos` | Logical value indicating if only positive markers should be returned.
`minPCT` | Numeric value indicating the minimum fraction of min.pct cells in which genes are detected. Default is `0.1`.
`threshUse` | Numeric value indicating the logFC threshold value on which on average, at least X-fold difference (log-scale) between the two groups of cells exists. Default is `0.25`.
`verbose` | Logical value indicating if informative messages should be displayed. Default is `TRUE`.

### Value

A `SingleCellExperiment` object that contains marker genes populated in a data.frame stored inside metadata slot.

[Package singleCellTK version 2.2.0 Index]