readIntensities {ShortRead}R Documentation

Read Solexa 'int' and 'nse' files

Description

readIntensities reads image `intensity' files (such as Solexa's _int.txt and (optionally) _nse.txt) in a directory into a single object.

Usage

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 (using, e.g., paste(pattern, intExtension, sep="") with intExtension or nseExtension 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 arugment type that determines how intensities are parsed. Use the type argument to readIntensities,character-method, as follows:

Arugments to these methods are as follows:

Value

An object derived from class Intensity.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

Examples

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)))

[Package ShortRead version 1.2.1 Index]