(Legacy) Read Illumina image intensity files

Description

readIntensities reads image ‘intensity’ files (such as Illumina's _int.txt and (optionally) _nse.txt) into a single object.

Usage

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readIntensities(dirPath, pattern=character(0), ...)

Arguments

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 with dirPath, as described below, to match files to be summarized.

...

Additional arguments used by methods.

Details

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="").

Value

An object derived from class Intensity.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>, Michael Muratet <mmuratet@hudsonalpha.org> (RTA).

Examples

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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(readIntensityInfo(int)))

## Not run: ## RTA Lane 2, cycles 1:80, cycle iteration 1, tile 3
int <- readIntensities("Data/Intensities", type="RtaIntensity",
                       lane=2, cycles=1:80, tiles=3)

## End(Not run)

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