readBaseQuality {ShortRead} | R Documentation |
readBaseQuality
reads all base call files in a directory
dirPath
whose file name matches seqPattern
and all quality
score files whose name matches prbPattern
, returning a compact
internal representation of the sequences, and quality scores in the files.
Methods read all files into a single R object.
readBaseQuality(dirPath, seqPattern=character(0), prbPattern=character(0), ...)
dirPath |
A character vector (or other object; see methods defined on this generic) giving the directory path (relative or absolute) of files to be input. |
seqPattern |
The (grep -style) pattern describing
base call file names to be read. The default (character(0) )
results in (attempted) input of all files in the directory. |
prbPattern |
The (grep -style) pattern describing
quality score file names to be read. The default (character(0) )
results in (attempted) input of all files in the directory. |
... |
Additional arguments, perhaps used by methods. |
A single R object (e.g., ShortReadQ
) containing
sequences and qualities of all files in dirPath
matching
seqPattern
and prbPattern
respectively. There is no
guarantee of order in which files are read.
Patrick Aboyoun <paboyoun@fhcrc.org>
A ShortReadQ
object.
sp <- SolexaPath(system.file("extdata", package="ShortRead")) readBaseQuality(sp, seqPattern="s_1.*_seq.txt", prbPattern="s_1.*_prb.txt")