create_scExp {ChromSCape} | R Documentation

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

### Description

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).

### Usage

    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)
    scExp

[Package ChromSCape version 1.2.62 Index]