DEGanalysis2clust: Determining differentially expressed genes (DEGs) between two particular clusters.

Description

This function defines DEGs between particular clusters generated by either K-means or model based clustering.

Usage

DEGanalysis2clust(
  object,
  K,
  Clustering = "K-means",
  fdr = 0.05,
  name = "Name",
  First = "CL1",
  Second = "CL2",
  export = FALSE,
  quiet = FALSE,
  plot = TRUE,
  filename_deg = "DEGsTable",
  filename_sigdeg = "sigDEG",
  ...
)
# S4 method for DISCBIO
DEGanalysis2clust(
  object,
  K,
  Clustering = "K-means",
  fdr = 0.05,
  name = "Name",
  First = "CL1",
  Second = "CL2",
  export = FALSE,
  quiet = FALSE,
  plot = TRUE,
  filename_deg = "DEGsTable",
  filename_sigdeg = "sigDEG",
  ...
)

Value

A list containing two tables.

Arguments

object: DISCBIO class object.
K: A numeric value of the number of clusters.
Clustering: Clustering has to be one of the following: ["K-means","MB"]. Default is "K-means"
fdr: A numeric value of the false discovery rate. Default is 0.05.
name: A string vector showing the name to be used to save the resulted tables.
First: A string vector showing the first target cluster. Default is "CL1"
Second: A string vector showing the second target cluster. Default is "CL2"
export: A logical vector that allows writing the final gene list in excel file. Default is TRUE.
quiet: if `TRUE`, suppresses intermediate text output
plot: if `TRUE`, plots are generated
filename_deg: Name of the exported DEG table
filename_sigdeg: Name of the exported sigDEG table
...: additional parameters to be passed to samr()