runCellQC: Perform QC on cells from 'RNAseq' object

Description Usage Arguments Value Author(s)

Description

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

Usage

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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)

Arguments

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.

Value

vector of logical values where TRUE = fail and FALSE = pass stored in runCellQC slot from RNAseq object.

Author(s)

Blanca Pijuan Sala.


BPijuanSala/proSeq documentation built on Oct. 10, 2018, 7:20 p.m.