| readFastq {ShortRead} | R Documentation |
readFastq reads all FASTQ-formated files in a directory
dirPath whose file name matches pattern pattern,
returning a compact internal representation of the sequences and
quality scores in the files. Methods read all files into a single R
object; a typical use is to restrict input to a single FASTQ file.
readFastq(dirPath, pattern=character(0), ...)
dirPath |
A character vector (or other object; see methods defined on this generic) giving the directory path (relative or absolute) of FASTQ files to be read. |
pattern |
The (grep-style) pattern describing file
names to be read. The default (character(0)) results in line
(attempted) input of all files in the directory. |
... |
Additional arguments, perhaps used by methods. |
The fastq format is not quite precisely defined. The basic definition used here parses the following four lines as a single record:
@HWI-EAS88_1_1_1_1001_499
GGACTTTGTAGGATACCCTCGCTTTCCTTCTCCTGT
+HWI-EAS88_1_1_1_1001_499
]]]]]]]]]]]]Y]Y]]]]]]]]]]]]VCHVMPLAS
The first and third lines are identifiers preceded by a specific
character (the identifiers are identical, in the case of Solexa). The
second line is an upper-case sequence of nucleotides. The parser
recognizes IUPAC-standard alphabet (hence ambiguous nucleotides),
coercing . to - to represent missing values. The final
line is an ASCII-encoded representation of quality scores, with one
ASCII character per nucleotide.
The encoding implicit in Solexa-derived fastq files is that each
character code corresponds to a score equal to the ASCII character
value minus 64 (e.g., ASCII @ is decimal 64, and corresponds to
a Solexa quality score of 0). This is different from BioPerl, for
instance, which recovers quality scores by subtracting 33 from the
ASCII character value (so that, for instance, !, with decimal
value 33, encodes value 0).
The BioPerl description of fastq asserts that the first character of
line 4 is a !, but the current parser does not support this
convention.
A single R object (e.g., ShortReadQ) containing
sequences and qualities contained in all files in dirPath
matching pattern. There is no guarantee of order in which files
are read.
Martin Morgan
The IUPAC alphabet in Biostrings.
http://www.bioperl.org/wiki/FASTQ_sequence_format for the BioPerl definition of fastq.
Solexa documentation `Data analysis - documentation : Pipeline output and visualisation'.
showMethods("readFastq")
sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
sread(rfq)
id(rfq)
quality(rfq)
## SolexaPath method 'knows' where FASTQ files are placed
rfq1 <- readFastq(sp, pattern="s_1_sequence.txt")
rfq1