Perform quality assessment on short reads
This function is a common interface to quality assessment functions
ShortRead. Results from this function may be
displayed in brief, or integrated into reports using, e.g.,
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A character vector or other object (e.g.,
A character vector limiting the files in
The type of file being parsed; must be a character vector of length 1, selected from one of the types enumerated in the parameter.
Additional arguments used by methods.
The most common use of this function provides a directory path and pattern identifying FASTQ files for quality assessment. The default is then to create a quality assessment report based on a random sample of n=1000000 reads from each file.
The following methods are defined, in addition to those on S4 formal classes documented elsewhere:
Quality assessment is performed on all files in directory
dirPathwhose file name matches
pattern. The type of analysis performed is based on the
SolexaExportwhen all files matching
Bowtiefor Bowtie files. Use
mapfiles produced by MAQ versions below 0.70 and
MAQMapfor more recent output. Use
fastqfor collections of fastq-format files. Quality assessment details vary depending on data source.
dirPathis a list of objects, all of the same class and typically derived from
ShortReadQ, on which quality assessment is performed. All elements of the list must have names, and these should be unique.
An object derived from class
contained in this object are meant for use by
Martin Morgan <email@example.com>
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