FindGlobalMarkers {IRISFGM} | R Documentation

## FindGlobalMarkers

### Description

FindGlobalMarkers

This function is for finding global marker FindGlobalMarkers is based on Seurat FindAllMarkers and the data from Tmp.seurat slots.

### Usage

    FindGlobalMarkers(object, ...)

    .findglobalMarkers(
      object = NULL,
      idents = NULL,
      logfc.threshold = 0.25,
      test.use = "wilcox",
      only.pos = TRUE,
      random.seed = 1,
      min.pct = 0.1
    )

    ## S4 method for signature 'IRISFGM'
    FindGlobalMarkers(
      object = NULL,
      idents = NULL,
      logfc.threshold = 0.25,
      test.use = "wilcox",
      only.pos = TRUE,
      random.seed = 1,
      min.pct = 0.1
    )

### Arguments

`object` | input IRIS-FGM object
`...` | other arguments passed to methods
`idents` | choose an idents for labelling cells
`logfc.threshold` | Limit testing to genes which show, on average, at least X-fold difference (log-scale) between the two groups of cells. Default is 0.25 Increasing logfc.threshold speeds up the function, but can miss weaker signals.
`test.use` | same as `FindAllMarkers`
`only.pos` | keep postive result
`random.seed` | set seed for reproducibility
`min.pct` | only test genes that are detected in a minimum fraction of min.pct cells in either of the two populations. Meant to speed up the function by not testing genes that are very infrequently expressed. Default is 0.1

### Value

Output is a differentially expressed gene list

### Examples

    data("example_object")
    markers <- FindGlobalMarkers(
    object = example_object,
    idents = "Seurat_r_0.8_k_20")

[Package IRISFGM version 1.2.0 Index]