DEGanalysis2clust {DIscBIO}

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 signature '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",
  ...
)

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()

Value

A list containing two tables.