Perform_DGE_ONEvsALL: A Perform_DGE_ONEvsALL Function
In parveendabas/SCA: What the Package Does (One Line, Title Case)

Perform_DGE_ONEvsALL

R Documentation

A Perform_DGE_ONEvsALL Function

Description

This function allows you to perform differential gene analysis.

Usage

Perform_DGE_ONEvsALL(
  Temp.object,
  saveDIR,
  SuffixName = "ALLcells",
  MainCol = "seurat_clusters",
  MainColOrder = ClusOrder,
  MainColPallete = ClusPallette,
  ColNamesToPlot = ColNamesToPlot,
  ColPaletteToPlot = ColPaletteToPlot,
  Species = "hsa",
  FDR = 0.1,
  FCcutoff = 1.5,
  topnumber = 5,
  min.pctagecells = 0.25,
  test.use = "wilcox",
  only.pos.Genes = TRUE,
  latent.vars = NULL,
  min.diff.pct = -Inf,
  downsampleHeatmap = 300,
  plots = TRUE,
  save = TRUE,
  ComputeDGEs = "YES"
)

Arguments

`Temp.object`	A list of Seurat objects between which to find anchors for downstream integration.
`saveDIR`	Path to save generated data.
`SuffixName`	Suffix. to be added in the directory name as
`MainCol`	Column to be used (Default is seurat_cluster)
`MainColOrder`	Factor order to be used (Default is numerical sorted order)
`MainColPallete`	color palette to be used
`ColNamesToPlot`	Vector of identities to plot
`ColPaletteToPlot`	list of color palettes to plot for the identities
`Species`	Species Name. Valid options are hsa or mmu
`FDR`	FDR cutoff
`FCcutoff`	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.
`topnumber`	Max #genes to be plotted per identity
`min.pctagecells`	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 0.25
`test.use`	Denotes which test to use.
`only.pos.Genes`	Only return positive markers (TRUE by default)
`latent.vars`	Variables to test, used only when test.use is one of 'LR', 'negbinom', 'poisson', or 'MAST'
`min.diff.pct`	only test genes that show a minimum difference in the fraction of detection between the two groups. Set to -Inf by default
`downsampleHeatmap`	Max #cells to be plotted per identity
`plots`	Save CCA plots
`save`	Save integrated CCA RDS Seurat object
`ComputeDGEs`	To run FindAllMarkers or not