FEAST {FEAST}R Documentation

FEAST main function

Description

FEAST main function

Usage

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

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.

BPPARAM

parameters for BiocParallel. e.g. bpparam() and SnowParam.

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)

[Package FEAST version 1.0.0 Index]