Closed aniketbroad2604 closed 2 years ago
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)
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?