mnnCorrect_cds: Performs mNN batch correction on PCA data from a cds

In scfurl/m3addon: This package adds to the popular "monocle3"

Usage

mnnCorrect_cds(
  cds,
  batch_term,
  fast = TRUE,
  k = 20,
  sigma = 0.1,
  cos.norm.in = TRUE,
  cos.norm.out = TRUE,
  svd.dim = 0L,
  var.adj = TRUE,
  compute.angle = FALSE,
  subset.row = NULL,
  order = NULL,
  pc.approx = FALSE,
  irlba.args = list()
)

Arguments

cds	Input cell_data_set object.
batch_term	variable in ColData (pData) of cds that informs the batch to be corrected
fast	Whether to perform fastMNN or mnnCorrect (see scran package)
min_expr	Numeric indicating expression threshold
exprs_bin	Boolean whether to bin genes by mean expression
exprs_cuts	Numeic indicating number of bins if using exprs_bin

Value

Updated cell_data_set object

scfurl/m3addon documentation built on Aug. 9, 2021, 5:30 p.m.