| qa {ShortRead} | R Documentation |
This function is a common interface to quality assessment functions
available in ShortRead. Results from this function may be
displayed in brief, or integrated into reports using, e.g.,
report.
qa(dirPath, ...)
dirPath |
A character vector or other object (e.g.,
SolexaPath; see showMethods, below) locating
the data for which quality assessment is to be performed. See help
pages for defined methods (by evaluating the example code, below)
for details of available methods. |
... |
Additional arguments used by methods. |
The following methods are defined:
dirPath="character", pattern="character",
type=c("SolexaExport", "Bowtie", "MAQMapShort", "fastq"), ...
Quality assessment is performed on all files in directory
dirPath whose file name matches pattern. The type of
analysis performed is based on the type argument. Use
SolexaExport when all files matching pattern are
Solexa _export.txt files. Use Bowtie for Bowtie
files. Use MAQMapShort for MAQ map files produced by
MAQ versions below 0.70, and fastq for collections of
fastq-format files. Quality assessment details vary depending on
data source.
An object derived from class .QA
Martin Morgan <mtmorgan@fhcrc.org>
.QA,
SolexaExportQA
MAQMapQA
FastqQA
showMethods("qa")