SuperCell (version 1.0)

supercell_estimate_velocity: Run RNAvelocity for super-cells (slightly modified from https://github.com/velocyto-team/velocyto.R) Not yet adjusted for super-cell size (not sample-weighted)

Description

Run RNAvelocity for super-cells (slightly modified from https://github.com/velocyto-team/velocyto.R) Not yet adjusted for super-cell size (not sample-weighted)

Usage

supercell_estimate_velocity(
  emat,
  nmat,
  smat = NULL,
  membership = NULL,
  supercell_size = NULL,
  do.run.avegaring = (ncol(emat) == length(membership)),
  kCells = 10,
  ...
)

Value

results of https://github.com/velocyto-team/velocyto.R plus metacell size vector

Arguments

emat

spliced (exonic) count matrix (see https://github.com/velocyto-team/velocyto.R)

nmat

unspliced (nascent) count matrix (https://github.com/velocyto-team/velocyto.R)

smat

optional spanning read matrix (used in offset calculations) (https://github.com/velocyto-team/velocyto.R)

membership

supercell membership ('membership' field of SCimplify)

supercell_size

a vector with supercell size (if emat and nmat provided at super-cell level)

do.run.avegaring

whether to run averaging of emat & nmat (if nmat provided at a single-cell level)

kCells

number of k nearest neighbors (NN) to use in slope calculation smoothing (see https://github.com/velocyto-team/velocyto.R)

...

other parameters from https://github.com/velocyto-team/velocyto.R