qc_filt: Filters raw gene expression data based on depth, unique...

In califano-lab/PISCES: Protein Activity Inferecne in Single Cells

Filters raw gene expression data based on depth, unique genes, and percentage of MT reads.

Description

Filters raw gene expression data based on depth, unique genes, and percentage of MT reads.

Usage

qc_filt(
  raw.counts,
  min.depth = 0,
  max.depth = Inf,
  min.genes = 0,
  max.genes = Inf,
  max.mt = 1,
  min.gene.count,
  species = c("hum", "mur"),
  genes = c("symb", "ensg")
)

Arguments

raw.counts	Matrix of raw gene expression data (features X samples).
min.depth	Minimum depth for each sample. Default of 0.
max.mt	Maximum percentage of Mitochondrial reads. Default of 1.
min.gene.count	Minimum total reads for a gene to be kept. If not specified, default is 0.01 * # of samples.
species	One of ‘c(’hum', 'mur')', specifying human or murine data respectively. If not specified, assumes human.
genes	One of ‘c(’symb', 'ensg')', specifying gene symbols or ENSG names respectively. If not specified, assumed symbols.

Value

Matrix of normalized counts (features X samples).

califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.