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]