ClustDiffGenes function

ClustDiffGenes

Creates a table of cluster differences

ClustDiffGenes(
  object,
  K,
  pValue = 0.05,
  fdr = 0.01,
  export = FALSE,
  quiet = FALSE,
  filename_up = "Up-DEG-cluster",
  filename_down = "Down-DEG-cluster",
  filename_binom = "binomial-DEGsTable",
  filename_sigdeg = "binomial-sigDEG"
)

## S4 method for signature 'DISCBIO'
ClustDiffGenes(
  object,
  K,
  pValue = 0.05,
  fdr = 0.01,
  export = FALSE,
  quiet = FALSE,
  filename_up = "Up-DEG-cluster",
  filename_down = "Down-DEG-cluster",
  filename_binom = "binomial-DEGsTable",
  filename_sigdeg = "binomial-sigDEG"
)

Arguments

• object: DISCBIO class object.
• K: A numeric value of the number of clusters.
• pValue: A numeric value of the p-value. Default is 0.05.
• fdr: A numeric value of the false discovery rate. Default is 0.01.
• export: A logical vector that allows writing the final gene list in excel file. Default is TRUE.
• quiet: if TRUE, suppresses intermediate text output
• filename_up: Name of the exported "up" file (if export=TRUE)
• filename_down: Name of the exported "down" file (if export=TRUE)
• filename_binom: Name of the exported binomial file
• filename_sigdeg: Name of the exported sigDEG file

Returns

A list containing two tables.

Examples

sc <- DISCBIO(valuesG1msTest)
sc <- Clustexp(sc, cln = 3, quiet = TRUE)
cdiff <- ClustDiffGenes(sc, K = 3, fdr = .3, export = FALSE)
str(cdiff)
cdiff[[2]]