create_scExp: Wrapper to create the single cell experiment from count...

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

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

raw <- create_scDataset_raw()
scExp = create_scExp(raw$mat, raw$annot)
scExp

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