readMage: Read DTT (MAGE) sample attribute files

In AffyCompatible: Affymetrix GeneChip software compatibility

Description

This functions reads the content of Affymetrix DTT (MAGE) sample attribute files created by GCOS. Objects are represented as R classes. Navigation and extraction of data are described in the vignette ‘Retrieving MAGE and ARR sample attributes’.

Usage

readMage(fls, ...)

Arguments

fls	A character vector containing the paths to files to be read.
...	Additional arguments, currently unused.

Value

An object or list of objects of class ArrayFileSet, depending on whether one or several file paths are provided.

Author(s)

Martin Morgan

See Also

The vignette ‘Retrieving MAGE and ARR sample attributes’ for detailed illustration of use.

xclass and readXml for advanced access methods.

Examples

dir <- system.file("extdata", "DTT", package="AffyCompatible")
fls <- list.files(dir, full=TRUE)
basename(fls)
readArr(fls[[1]])

Example output

Loading required package: XML
Loading required package: RCurl
Loading required package: bitops
[1] "MPRO_0hr_A.xml"                "Sample_1_Wash_Stain_Param.xml"
[3] "Sample_2_4C_Scan.xml"         
identifier: Affymetrix.com 
name:  
propertySets_assnlist: PropertySets_assnlist(1)
auditAndSecurity_package: AuditAndSecurity_package(1)
protocol_package: Protocol_package(1)
bioMaterial_package: BioMaterial_package(1)
arrayDesign_package: ArrayDesign_package(1)
array_package: Array_package(1)
bioAssay_package: BioAssay_package(1)
bioAssayData_package: BioAssayData_package(1)
experiment_package: Experiment_package(1)

AffyCompatible documentation built on Nov. 8, 2020, 8:15 p.m.