FEAST {FEAST} | R Documentation |
FEAST main function
FEAST( Y, k = 2, num_pcs = 10, dim_reduce = c("irlba", "svd", "pca"), split = FALSE, batch_size = 1000, nProc = 1 )
Y |
A expression matrix. Raw count matrix or normalized matrix. |
k |
The number of input clusters (best guess). |
num_pcs |
The number of top pcs that will be investigated through the consensus clustering. |
dim_reduce |
dimension reduction methods chosen from pca, svd, or irlba. |
split |
boolean. If T, using subsampling to calculate the gene-level significance. |
batch_size |
when split is true, need to claim the batch size for spliting the cells. |
nProc |
number of cores for BiocParallel enviroment. |
the rankings of the gene-significance.
data(Yan) k = length(unique(trueclass)) set.seed(123) rixs = sample(nrow(Y), 500) cixs = sample(ncol(Y), 40) Y = Y[rixs, cixs] ixs = FEAST(Y, k=k)