create_scDataset_raw {ChromSCape} | R Documentation |
Create a simulated single cell datamatrix & cell annotation
create_scDataset_raw( cells = 300, features = 600, featureType = c("window", "peak", "gene"), sparse = TRUE, nsamp = 4, ref = "hg38", batch_id = factor(rep(1, nsamp)) )
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)) |
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
# 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)