qualityReportSFF {R453Plus1Toolbox} | R Documentation |
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.
qualityReportSFF(sfffiles, outfile)
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. |
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
.
Christian Ruckert
## Not run: file <- system.file("extdata", "SFF", "example.sff", package="R453Plus1Toolbox") qualityReportSFF(file, "QualityReport.pdf") ## End(Not run)