readIntensities {ShortRead} | R Documentation |
readIntensities
reads image `intensity' files (such as Solexa's
_int.txt
and (optionally) _nse.txt
) in a directory into
a single object.
readIntensities(dirPath, pattern=character(0), ...)
dirPath |
Directory path or other object (e.g.,
SolexaPath for which methods are defined. |
pattern |
A length 1 character vector representing a regular
expression to be combined (using, e.g., paste(pattern,
intExtension, sep="") with intExtension or
nseExtension to match files to be summarized. |
... |
Additional arguments used by methods. |
Additional methods are defined on specific classes, see, e.g.,
SolexaPath
.
The readIntensities,character-method
contains an arugment
type
that determines how intensities are parsed. Use the
type
argument to readIntensities,character-method
, as
follows:
type="IparIntensity"
Intensities are read from Solexa _pos.txt
,
_int.txt.p
, _nse.txt.p
-style file triplets. The
signature for this method is
dirPath, pattern=character(0), ...,
type="IparIntensity",
intExtension="_int.txt.p.gz",
nseExtension="_nse.txt.p.gz",
posExtension="_pos.txt",
withVariability=TRUE, verbose=FALSE
type="SolexaIntensity"
Intensities are read from Solexa _int.txt
and
_nse.txt
-style files; see SolexaPath
for details. The signature for this method is
dirPath, pattern=character(0), ...,
type="SolexaIntensity",
intExtension="_int.txt",
nseExtension="_nse.txt",
withVariability=TRUE, verbose=FALSE
Arugments to these methods are as follows:
character(1)
values pasted (with sep=""
) to pattern
to
identify different file sources._nse
files).
An object derived from class Intensity
.
Martin Morgan <mtmorgan@fhcrc.org>
fl <- system.file("extdata", package="ShortRead") sp <- SolexaPath(fl) int <- readIntensities(sp) int intensity(int)[1,,] # one read intensity(int)[[1:2,,]] # two reads, as 'array' head(rowMeans(intensity(int))) # treated as 'array' head(pData(readInfo(int)))