Additional methods are defined on specific classes, see, e.g.,
SolexaPath
.
The readIntensities,character-method
contains an argument
type
that determines how intensities are parsed. Use the
type
argument to readIntensities,character-method
, as
described below. All readIntensities,character
methods accepts
the folling arguments:
- withVariability:
- Include estimates of variability (i.e., from
parsing
_nse
files).
verbose:Report on progress when starting to read each file.
The supported types and their signatures are:
type="RtaIntensity"
Intensities are read from Illumina _cif.txt
and
_cnf.txt
-style files. The signature for this method is
dirPath, pattern=character(0), ..., type="RtaIntensity",
lane=integer(0), cycles=integer(0), cycleIteration=1L,
tiles=integer(0),
laneName=sprintf("L
cycleNames=sprintf("C
tileNames=sprintf("s_
posNames=sprintf("s_
withVariability=TRUE, verbose=FALSE
lane:integer(1)
identifying the lane in which
cycles and tiles are to be processed.
cycles:integer()
enumerating cycles to be
processed.
cycleIteration:integer(1)
identifying the
iteration of the base caller to be summarized
tiles:integer()
enumerating tile numbers to be
summarized.
laneName, cycleNames, tileNames,
posNames:character()
vectors identifying the lane and
cycle directories, and the pos and tile file names
(excluding the .cif or .cnf extension) to be
processed.
The dirPath
and pattern
arguments are combined as
list.files(dirPath, pattern)
, and must identify a single
directory. Most uses of this function will focus on a single tile
(specified with, e.g., tiles=1L
); the laneName
,
cycleNames
, tileNames
, and posNames
parameters are designed to work with the default Illumina pipeline
and do not normally need to be specified.
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
Files to be parsed are determined as, e.g., paste(pattern,
intExtension, sep="")
.
type="SolexaIntensity"
Intensities are read from Solexa _int.txt
and
_nse.txt
-style files. The signature for this method is
dirPath, pattern=character(0), ...,
type="SolexaIntensity",
intExtension="_int.txt",
nseExtension="_nse.txt",
withVariability=TRUE, verbose=FALSE
Files to be parsed are determined as, e.g., paste(pattern,
intExtension, sep="")
.