runCicero: runCicero

In plantformatics/Socrates: Analysis of scATAC-seq data

runCicero

Description

This function is a wrapper for several cicero commands

Usage

runCicero(
  cds,
  genome = NULL,
  k = 30,
  win = 5e+05,
  sample_num = 100,
  silent = TRUE
)

Arguments

cds	cicero object. Required.
genome	path to genome file. See 'inst/extdata/genome' for an example. Required.
k	numeric. Number of nearest neighbors for binning cells. See cicero for more details. Defaults to 30.
win	numeric. Window size for constraining co-accessible ACRs. Defaults to 500000.
sample_num	numeric. Number of random windows to sample for determining distance_parameter during 'run_cicero'. See cicero for more details.
silent	logical. Defaults to TRUE.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.