create_scDataset_raw: Create a simulated single cell datamatrix & cell annotation

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Create a simulated single cell datamatrix & cell annotation

Description

Create a simulated single cell datamatrix & cell annotation

Usage

create_scDataset_raw(
  cells = 300,
  features = 600,
  featureType = c("window", "peak", "gene"),
  sparse = TRUE,
  nsamp = 4,
  ref = "hg38",
  batch_id = factor(rep(1, nsamp))
)

Arguments

cells	Number of cells (300)
features	Number of features (600)
featureType	Type of feature (window)
sparse	Is matrix sparse ? (TRUE)
nsamp	Number of samples (4)
ref	Reference genome ('hg38')
batch_id	Batch origin (factor((1,1,1,1))

Value

A list composed of * mat : a sparse matrix following an approximation of the negative binomial law (adapted to scChIPseq) * annot : a data.frame of cell annotation * batches : an integer vector with the batch number for each cell

Examples

# Creating a basic sparse 600 genomic bins x 300 cells matrix and annotation
l = create_scDataset_raw()
head(l$mat)
head(l$annot)
head(l$batches)

# Specifying number of cells, features and samples
l2 = create_scDataset_raw(cells = 500, features = 500, nsamp=2)

# Specifying species
mouse_l = create_scDataset_raw(ref="mm10")

# Specifying batches
batch_l = create_scDataset_raw(nsamp=4, batch_id = factor(c(1,1,2,2)))

# Peaks of different size as features
peak_l = create_scDataset_raw(featureType="peak")
head(peak_l$mat)

# Genes as features
gene_l = create_scDataset_raw(featureType="gene")
head(gene_l$mat)

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.