R453Plus1Toolbox (version 1.22.0)

qualityReportSFF: 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.

Examples

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