DIscBIO (version 1.2.2)

DEGanalysis: Determining differentially expressed genes (DEGs) between all individual clusters.

Description

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

Usage

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

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()