DIscBIO (version 1.2.2)

ClustDiffGenes: ClustDiffGenes

Description

Creates a table of cluster differences

Usage

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 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"
)

Value

A list containing two tables.

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

Examples

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