runQA: Performs quality checks

In nixstix/RNASeqAnalysis: Analysis of RNA-Seq data: QC filtering, expression analysis, differential expression pipeline

Description

The function checks each fastq file specified in the "data file" for quality, and writes findings to a report.

Usage

runQA(dataFile, preFilter = TRUE)

Arguments

dataFile	An R data frame with the data to be processed. The R object is a standard format, and must contain the following headings: File, PE, Sample, Replicate, FilteredFile. More information about the file is available at datafileTemplate.
preFilter	A logical - if true (default), the function will select and analyse files which have not yet been processed for quality. If false, the function will select and analyse those files which have been processed for quality, i.e. the "filtered file" in the data file.

Details

The function should be run in the working directory, where all fastq files are found.

runQA iterates over each file specified in the "datafile". It runs a quality assessment from the ShortRead package. The ShortRead package (https://bioconductor.org/packages/release/bioc/html/ShortRead.html) contains more information about this step. The quality assessment may be performed before and after the filtering step, by setting the "pre-filter" parameter to true or to false, respectively. All quality assessment data is output to the "QA" directory. Quality reports are output to the working directory (under the QA directory). R objects of the raw data used to generate the reports are also saved to this directory.

Value

FastqQA object. Outputs quality results in the form of raw data (an R FastqQA object) and HTML format (saved to "QA" directory).

nixstix/RNASeqAnalysis documentation built on May 23, 2019, 7:06 p.m.