This class represents the directory location where Roche (454) result files (fasta sequences and qualities) can be found.
RochePath
constructor: RochePath(experimentPath = NA_character_,
readPath = experimentPath,
qualPath = readPath, ..., verbose = FALSE)
character(1) or
RochePath pointing to the top-level directory
of a Roche experiment.character() of directories (typically in
experimentPath) containing sequence (read) information. The
default selects all directories matching
list.files(experimentPath, "run").character() of directories (typically in
experimentPath) containing quality information. The default
selects all directories matching list.files(experimentPath,
"run").logical(1) indicating whether invalid paths
should be reported interactively.RocheSet has the following slots:
readPath:"character", as
described in the constructor, above.qualPath:"character", as
described in the constructor, above.basePath:"character",
containing the experimentPath."ExperimentPath", directly.
Class ".Roche", directly.
Class ".ShortReadBase", by class "ExperimentPath", distance 2.
Class ".ShortReadBase", by class ".Roche", distance 2.RochePath has the following methods or functions defined:
signature(dirPath = "RochePath",
pattern=".\.fna$", sample = 1, run = 1, ...): Read sequences
from files matching list.files(dirPath, pattern) (when
dirPath="character") or
list.files(readPath(dir)[run], pattern)[sample]. The
result is a DNAStringSet.signature(dirPath = "RochePath", reads=NULL,
pattern="\.qual$", sample=1, run=1, ...): Read quality scores
from files matching
list.files(qualPath(dirPath)[run])[sample]. Non-null
reads is used as an (optional) template for parsing
quality scores. signature(dirPath = "RochePath",
fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1,
run = 1): read sequences and quality scores into a
ShortReadQ instance.signature(dirPath = "character",
fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1,
run = 1): wrapper for method above, coercing dirPath
to a RochePath via RochePath(dirPath).signature(dirPath = "RochePath", ...):
Reads in base and quality information. Currently delegates to
readFastaQual, above, but will do more after
RochePath supports more file types.
signature(dirPath = "RochePath", ...): Pass
arguments on to readFastaQual, documented above. signature(object = "RochePath"): return the
contents of the readPath slot.signature(object = "RochePath"): return the
basenames of readPath(object).signature(path = "RochePath"): create a
RocheSet from path.signature(object = "RochePath"): Briefly
summarize the experiment path locations.signature(x = "RochePath"): Provide
additional detail on the Roche path. All file paths are presented
in full. ExperimentPath.