PrepareLqCellsData: Prepare data.frame for low-quality cells filtration. The more...

In kharchenkolab/dropestr: Preprocessing of Droplet-Based Single-Cell RNA-Seq Data

Description

Prepare data.frame for low-quality cells filtration. The more parameters provided, the more detailed matrix returned.

Usage

PrepareLqCellsData(
  count.matrix,
  aligned.reads.per.cell,
  total.umis.per.cell = NULL,
  total.reads.per.cell = NULL,
  intergenic.reads.per.cell = NULL,
  mitochondrion.fraction = NULL,
  scale = TRUE
)

PrepareLqCellsDataPipeline(
  data,
  total.reads.per.cell = NULL,
  merge.targets = NULL,
  mitochondrion.genes = NULL,
  mit.chromosome.name = NULL,
  scale = TRUE
)

Arguments

count.matrix	Matrix with counts of umi per gene per cell
aligned.reads.per.cell
total.umis.per.cell	(default=NULL)
total.reads.per.cell	Number of reads per cell before alignment (default=NULL)
intergenic.reads.per.cell	Number of intergenic reads per cell (default=NULL)
mitochondrion.fraction	Fraction of mitochondrion reads or UMIs per cell (default=NULL)
scale	(default=TRUE)
data	data, extracted with the pipeline.
merge.targets	Targets of CB merge. Used only with total.reads.per.cell provided.
mitochondrion.genes	(default=NULL)

Value

Data.frame for low-quality cells filtration

Functions

• PrepareLqCellsDataPipeline: wrapper for the data, obtained with the dropEst pipeline.

kharchenkolab/dropestr documentation built on Sept. 18, 2020, 2:14 a.m.