genQC: Plot Quality Checking Information for Sequencing Data

In Repitools: Epigenomic tools

Description

A series of quality control plots for sequencing data are made.

Usage

  ## S4 method for signature 'character'
genQC(qc.data, ...)
  ## S4 method for signature 'SequenceQCSet'
genQC(qc.data, expt = "Experiment")

Arguments

qc.data	A vector of character strings, each containing an absolute path to an RData file of a SequenceQC object, or a SequenceQC set object.
expt	The names of the experiments which the lanes are about.
...	The expt argument, which is not directly used in the character method.

Details

qc.data can be named, in which case this gives the names of the lanes used in the plotting. Otherwise the lanes will be given the names "Lane 1", "Lane 2", ..., "Lane n".

Value

The function is called for its output. The output is multiple pages, so the pdf device should be called before this function is.

Author(s)

Dario Strbenac

References

FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/

Examples

  ## Not run: 
    qc.files <- list.files(qc.dir, "QC.*RData", full.names = TRUE)
    genQC(qc.files, "My Simple Experiment")
  
## End(Not run)

Repitools documentation built on Nov. 8, 2020, 7:52 p.m.