qcFunc: Quality control function
In wjawaid/bglab: Berthold Gottgens lab scRNA seq

Description Usage Arguments Details Value Author(s)

Quality control function

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qcFunc(counts, ercc.data, htseqQC, geneTable, meta, metaLaneID = "flowCell",
  mitochondrialIdenitifier = "^mt|^MT", pdf = NULL, cutoffs = c(2e+05,
  0.2, 0.2, 0, 0, 1, 0))

`counts`	raw counts
`ercc.data`	Spike in data
`htseqQC`	HTseq output
`geneTable`	Genetable
`meta`	Metadata dataframe
`metaLaneID`	Lane that contains flowcell lane information
`mitochondrialIdenitifier`	Prefix for mitochondrial genes in geneTable
`pdf`	Name of output pdf
`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).