runCellQC: Perform QC on cells from 'RNAseq' object
In BPijuanSala/proSeq: Tools to preprocess RNA-seq data

Description Usage Arguments Value Author(s)

It performs QC on cells from countsRaw slot within the RNAseq object provided. It follows Brennecke et al., Nature Methods, 2013.

runCellQC(object, annTable = geneTable, geneInput = "ID",
  GeneDetection = 2, minMapreads = 2e+05, maxMapmit = 0.1,
  maxMapSpike = 0.5, minGenesExpr = 4000, checkCountsFeat = TRUE,
  outputPlots = "./", plotting = "pdf", passCol = "grey70",
  failCol = "red", thresCol = "blue", lty = 3, lwd = 2)

## S4 method for signature 'RNAseq'
runCellQC(object, annTable = geneTable,
  geneInput = "ID", GeneDetection = 2, minMapreads = 2e+05,
  maxMapmit = 0.1, maxMapSpike = 0.5, minGenesExpr = 4000,
  checkCountsFeat = TRUE, outputPlots = "./", plotting = "pdf",
  passCol = "grey70", failCol = "red", thresCol = "blue", lty = 3,
  lwd = 2)

`object`	`RNAseq` object.
`annTable`	Associative matrix or dataframe where column 1 reflects geneIDs and column2 the associated geneName. Default: Mus musculus geneTable (??geneTable).
`geneInput`	It states whether the genes in the counts table are IDs ("ID") or associated gene names ("name"). Note that IDs will refer to column 1 of annTable and names to column 2 of annTable. In the case of "names": if the ID is not found, the gene will be discarded. Default: ID (recommended).
`GeneDetection`	How many reads in a gene are needed to consider a gene detected in a cell. Default: 2. Important for nDetectedGenes plot.
`minMapreads`	Minimum number of reads mapping to nuclear genes. Default: 200,000. Check the nNuclearGenes plot. Important: This plot is log-scaled.
`maxMapmit`	Maximum percentage mapped mitochondrial reads. Default: 0.1. Check the fMapped2Mit plot.
`maxMapSpike`	Maximum percentage of mapped spikeins. Default: 0.5.If no gene is spike-in, this condition will not be taken into account. Check the fMapped2ERCCs plot.
`minGenesExpr`	Minimum number of genes expressed in one cell at least. Default: 4000. Check nDetectedGenes plot.
`checkCountsFeat`	Logical (TRUE/FALSE). Specifies whether the QC should take into account the features of the mapping. Default = TRUE (recommended).
`outputPlots`	state directory where you want to output the plots. Default: Current directory.
`plotting`	It states whether plots are generated or not and you should specify the type. Options: "pdf", "tiff", "no". Default: "pdf". Default: TRUE
`passCol`	Plotting parameter. Color for cells that have passed QC. Default: "grey70"
`failCol`	Plotting parameter. Color for cells that have passed QC. Default: "red".
`thresCol`	Plotting parameter. Color for threshold line. Default: "blue".
`lty`	Plotting parameter. Line shape for threshold. For further information see `par`. Default: 3.
`lwd`	Plotting parameter. Line width for threshold.For further information see `par`. Default: 2.