simData: Multi-scenario simulator of single-cell epigenomic data

In plbaldoni/scChIPseqsim: Single-cell ChIP-seq Data Simulator Based on Pseudo-bulk Profiles

Description

Add description here

Usage

simData(
  refList,
  cellList,
  noiseList,
  depthList,
  relDepthList,
  label,
  path,
  genome,
  binSize,
  cores = 1,
  shuffleProp = NULL,
  shuffleChunks = 5000,
  ...
)

Arguments

refList	either a list of GenomicRanges (each element specifies the cluster's peaks) or a list of bam paths (each element specifies the alignment to generate data from)
cellList	list of size length(refList) with the number of cells per cluster
noiseList	list of size length(refList) with cluster-specific vectors of noise values from each cell
depthList	list of size length(refList) with the baseline number of cells per cluster
relDepthList	list of size length(refList) with cluster-specific vectors of relative depth values from each cell
label	a character with the data label
path	a character with the path where the simulated data will be saved
genome	a character specifying the target genome
binSize	integer with the size of the bin window
cores	number of cores for parallel computing
shuffleProp	either NULL (default) or the proportion of the genome to be shuffled (only applicable for scChIPseqFromBam)
shuffleChunks	size of the chunks that will be swapped across the genome (applicable for scChIPseq data only)
...	Arguments to pass to the scChIPseqsim constructor.

Details

Add details here

Value

Add return here

Author(s)

Pedro L. Baldoni, [e-mail]

plbaldoni/scChIPseqsim documentation built on June 11, 2020, 7:41 p.m.