performQC: Perform QC on data

In wjawaid/bglab: Berthold Gottgens lab scRNA seq

Description

Perform QC on data

Usage

performQC(object, selectedCells = "ALL", cutoffs = c(2e+05, 0.2, 0.2, 0, 0,
  1, 0), metaLaneID = "flowCell", mitochondrialIdenitifier = "^mt|^MT",
  pdf = NULL, qcFeatures = "ALL")

Arguments

object	SCD
selectedCells	Default "ALL". If data not available on all cells give subset.
cutoffs	Default 2e5, 0.2, 0.2, 0, 0, 1, 0. Set thresholds for: number of mapped reads (greater than threshold), ratio of genes to total number of reads (greater than threshold), ratio of mitchondrial genes to mitochondrial + nuclear genes (less than threshold), number of nuclear genes (greater than threshold), number of genes with >10 reads per million (greater than threshold), ercc:mapped (less than threshold) and nuclearGenes:mapped (greater than threshold).
metaLaneID	ID of column that contains information about flow cell lane.
mitochondrialIdenitifier	Regexp identifying mitochondrial gene in geneTable
pdf	Prefix name of pdfs.
qcFeatures	Features from the QC to plot.

Details

Perform QC on data

Value

SCD object

Author(s)

Wajid Jawaid

wjawaid/bglab documentation built on May 4, 2019, 6:33 a.m.