findMarkers function

Find marker genes for each cluster

This function takes an object of class iCellR and performs differential expression (DE) analysis to find marker genes for each cluster.

findMarkers(
  x = NULL,
  data.type = "main",
  pval.test = "t.test",
  p.adjust.method = "hochberg",
  fold.change = 2,
  padjval = 0.1,
  low.cell.filt = 5,
  Inf.FCs = FALSE,
  uniq = FALSE,
  positive = TRUE
)

Arguments

• x: An object of class iCellR.
• data.type: Choose from "main", "atac", "atac.imputed" and "imputed", default = "main"
• pval.test: Choose from "t.test", "wilcox.test", default = "t.test".
• p.adjust.method: Correction method. Choose from "holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr", "none", default = "hochberg".
• fold.change: A number that designates the minimum fold change for out put, default = 2.
• padjval: Minimum adjusted p value for out put, default = 0.1.
• low.cell.filt: filter out clusters with low number of cells, default = 5.
• Inf.FCs: If set to FALSE the infinite fold changes would be filtered from out put, default = FALSE.
• uniq: If set to TRUE only genes that are a marker for only one cluster would be in the out put, default = FALSE.
• positive: If set to FALSE both the up regulated (positive) and down regulated (negative) markers would be in the out put, default = TRUE.

Returns

An object of class iCellR