Wrapper to create the single cell experiment from count matrix and feature dataframe

Create the single cell experiment from (sparse) datamatrix and feature dataframe containing feature names and location. Also optionally removes zero count Features, zero count Cells, non canconical chromosomes, and chromosome M. Calculates QC Metrics (scran).

create_scExp(
  datamatrix,
  annot,
  remove_zero_cells = TRUE,
  remove_zero_features = TRUE,
  remove_non_canonical = TRUE,
  remove_chr_M = TRUE,
  mainExpName = "main",
  verbose = TRUE
)

Arguments

datamatrix	A matrix or sparseMatrix of raw counts. Features x Cells (rows x columns).
annot	A data.frame containing informations on cells. Should have the same number of rows as the number of columns in datamatrix.
remove_zero_cells	remove cells with zero counts ? (TRUE)
remove_zero_features	remove cells with zero counts ? (TRUE)
remove_non_canonical	remove non canonical chromosomes ?(TRUE)
remove_chr_M	remove chromosomes M ? (TRUE)
mainExpName	Name of the mainExpName e.g. 'bins', 'peaks'... ("default")
verbose	(TRUE)

Value

Returns a SingleCellExperiment object.

Examples

scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot)
#> ChromSCape::create_scExp - the matrix has 300 cells and 600 features.
scExp
#> class: SingleCellExperiment 
#> dim: 600 300 
#> metadata(0):
#> assays(1): counts
#> rownames(600): chr1_1_5147117 chr1_5147118_10294233 ...
#>   chrX_89737519_94884635 chrX_94884636_100031751
#> rowData names(1): ID
#> colnames(300): sample_1_c1 sample_1_c2 ... sample_4_c69 sample_4_c70
#> colData names(5): barcode cell_id sample_id batch_id total_counts
#> reducedDimNames(0):
#> mainExpName: main
#> altExpNames(0):