(Legacy) Read Solexa prb files as fastq-style quality scores
readPrb reads all _prb.txt files in a directory into a
single object. Most methods (see details) do this by identifying the
maximum base call quality for each cycle and read, and representing
this as an ASCII-encoded character string.
readPrb(dirPath, pattern = character(0), ...)
dirPath |
Directory path or other object (e.g.,
|
pattern |
Regular expression matching names of |
... |
Additional arguments, unused. |
The readPrb,character-method contains an argument as
that determines the value of the returned object, as follows.
as="SolexaEncoding"The ASCII encoding of the maximum per cycle and read quality score is encoded using Solexa conventions.
as="FastqEncoding"The ASCII encoding of the maximum per cycle and read quality score
is encoded using Fastq conventions, i.e., ! has value 0.
as="IntegerEncoding"The maximum per cycle and read quality score is returned as a in integer value. Values are collated into a matrix with number of rows equal to number of reads, and number of columns equal to number of cycles.
as="array"The quality scores are not summarized; the return value is an integer array with dimensions corresponding to reads, nucleotides, and cycles.
An object of class QualityScore, or an integer matrix.
Martin Morgan <mtmorgan@fhcrc.org>
fl <- system.file("extdata", package="ShortRead")
sp <- SolexaPath(fl)
readPrb(sp, "s_1.*_prb.txt") # all tiles to a single filePlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.