DEGanalysis2clust {DIscBIO} | R Documentation |
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 |
|
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.