FEAST: FEAST main function

In suke18/FEAST: FEAture SelcTion (FEAST) for Single-cell clustering

Description

FEAST main function

Usage

FEAST(
  Y,
  k = 2,
  num_pcs = 10,
  dim_reduce = c("irlba", "svd", "pca"),
  split = FALSE,
  batch_size = 1000,
  nProc = 1
)

Arguments

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.

Value

the rankings of the gene-significance.

Examples

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)

suke18/FEAST documentation built on Sept. 14, 2021, 12:22 a.m.