optimal_rank {ccfindR} | R Documentation |
Takes as main argument scNMFSet
object containing factorized output
and estimate the optimal rank.
optimal_rank(object, df = 10, BF.threshold = 3, type = NULL, m = NULL)
object |
|
df |
Degrees of freedom for split fit. Upper bound is the total number of data points (number of rank values scanned). |
BF.threshold |
Bayes factor threshold for statistical threshold. |
type |
|
m |
Number of features (e.g., genes) in the count matrix. Only necessary when
|
The input object is used along with Bayes factor threshold to determine the
heterogeneity type (1 or 2) and the optimal rank.
If evidence(rank 1)/evidence(rank2) > BF.treshold
, rank 1 is favorable than rank 2.
List containing type
and ropt
(optimal rank).
set.seed(1) x <- simulate_whx(nrow=50, ncol=100, rank=5) s <- scNMFSet(x$x) s <- vb_factorize(s, ranks=seq(2,8), nrun=5) plot(s) optimal_rank(s)