Repitools (version 1.18.0)

genQC: Plot Quality Checking Information for Sequencing Data

Description

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

Usage

"genQC"(qc.data, ...) "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.

Value

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

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".

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)