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")