create_scDataset_raw {ChromSCape} | R Documentation

## 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)

[Package ChromSCape version 1.2.62 Index]