qualityReportSFF {R453Plus1Toolbox} | R Documentation

## Function To Create A Quality Report In PDF Format

### Description

This function takes a character vector consisting of filenames pointing to files in Roche's SFF format as input and creates a quality report in PDF format as output.

### Usage

    qualityReportSFF(sfffiles, outfile)

### Arguments

`sfffiles` | A character vector of the SFF files to read in.
`outfile` | The name of the PDF report file created. Defaults to ‘qcreport.pdf’ in the current directory.

### Details

The function uses the qualityReport.Rnw file from the extdata directory of the package and `Sweave` to create a .tex file which is afterwards converted to .pdf format. In the .Rnw file the following quality control functions are used: `readLengthStats`, `readLengthHist`, `baseQualityStats`, `baseQualityHist`, `sequenceQualityHist`, `positionQualityBoxplot`, `baseFrequency`, `nucleotideCharts`, `gcContent`, `gcPerPosition`, `gcContentHist`, `complexity.dust`, `complexity.entropy`, `dinucleotideOddsRatio`.

### Author(s)

Christian Ruckert

### Examples

      ## Not run:
        file <- system.file("extdata", "SFF", "example.sff", package="R453Plus1Toolbox")
        qualityReportSFF(file, "QualityReport.pdf")

    ## End(Not run)

[Package R453Plus1Toolbox version 1.28.1 Index]