extracting gene list from a specific cluster

[aniketbroad2604]

I am having trouble in extracting the gene list which belong to a specific cluster. Is there a code or function which is already present to extract the genes?

[dchiu911]

Hi @aniketbroad2604 please try the following reprex. If your input matrix data has rownames, then the resulting final assignment matrix will also show the mapping in the clusters element of obj. If you are interested in clustering genes instead of samples the input can be transposed.

library(diceR)
data(hgsc)
hgsc <- hgsc[1:100, 1:50]
obj <- dice(
  hgsc,
  nk = 4,
  reps = 5,
  algorithms = c("ap", "sc", "block", "som", "cmeans", "hdbscan"),
  cons.funs = c("kmodes", "majority")
)
#> Selecting k and imputing non-clustered cases
#> Computing consensus functions
#> Evaluating output with consensus function results
#> Diverse Cluster Ensemble Completed
head(obj$clusters)
#>                     kmodes majority
#> TCGA.04.1331_PRO.C5      2        2
#> TCGA.04.1332_MES.C1      1        2
#> TCGA.04.1336_DIF.C4      4        1
#> TCGA.04.1337_MES.C1      1        1
#> TCGA.04.1338_MES.C1      4        4
#> TCGA.04.1341_PRO.C5      2        2

obj_t <- dice(
  t(hgsc),
  nk = 4,
  reps = 5,
  algorithms = c("ap", "sc", "block", "som", "cmeans", "hdbscan"),
  cons.funs = c("kmodes", "majority")
)
#> Selecting k and imputing non-clustered cases
#> Computing consensus functions
#> Evaluating output with consensus function results
#> Diverse Cluster Ensemble Completed
head(obj_t$clusters)
#>        kmodes majority
#> ABAT        3        1
#> ABHD2       1        1
#> ACTB        1        1
#> ACTR2       3        1
#> ACTR5       1        1
#> ACVR2A      3        1

^{Created on 2022-08-16 by the reprex package (v2.0.1)}