CalculateSeuratQC: Calculate some QC metrics

In lyc-1995/MySeuratWrappers: My extentions to Seurat package

Description

Compute quality control (QC) metrics for each control feature and cell in a Seurat object, accounting for specified control sets.

Usage

CalculateSeuratQC(
  object,
  assay = NULL,
  calculate.mapped.reads = FALSE,
  mol.info = NULL,
  total.reads = NULL,
  control.feature.list = NULL,
  use.names = FALSE,
  symbol.to.id = NULL,
  log10 = TRUE
)

Arguments

object	Seurat object
assay	Name of assay to use
calculate.mapped.reads	Whether or not to calculate mapped reads metrics. Default is FALSE. If TRUE, will need to set molecule information
mol.info	Molecule information for mapped reads calculation (molecule_info.h5 files of 10x)
total.reads	a data.frame with column named 'total.reads', collecting total count of reads per barcode.This can be extracted from .BAM file that CellRanger output and is used to calculate mapping rate per cell.
control.feature.list	A list containing one or more vectors (a character vector of ensembl IDs named by feature symbols), used to identify feature controls
use.names	Whether or not to use feature names instead of ID. If FALSE, shall specify symbol.to.id data.frame for transferation
symbol.to.id	Data.frame for convertion from gene symbols to such as ENSEMBL ID, must contain at least two columns (use 'ID' and 'Symbol' as colnames)
log10	Whether or not to calculate log10 transformed QC metrics

Value

Returns Seurat object with new meta.data storing QC metrics

lyc-1995/MySeuratWrappers documentation built on June 30, 2020, 11:48 a.m.