FindGlobalMarkers: FindGlobalMarkers

In carter-allen/IRISFGM: Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

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

## Not run: 
Global_marker <- FindGlobalMarkers(object,
idents = "Seurat0.6",
logfc.threshold = 0.25,
test.use = "wilcox"
)
## End(Not run)

carter-allen/IRISFGM documentation built on Dec. 31, 2020, 9:54 p.m.