### R code from vignette source 'vignettes/RMAGEML/inst/doc/RMAGEML.Rnw'

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### code chunk number 1: RMAGEML.Rnw:92-94
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## load up the library
library(RMAGEML)


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### code chunk number 2: RMAGEML.Rnw:105-109
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## create marrayRaw object
datadir <- system.file("MAGEMLdata", package="RMAGEML")
raw <- importMAGEML(directory = datadir, package = "marray", arrayID = "A-MEXP-14", DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median")
print(raw)


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### code chunk number 3: RMAGEML.Rnw:114-119
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## create marrayRaw object
datadir <- system.file("MAGEMLdata", package="RMAGEML")
if(interactive()){
raw <- importMAGEML(directory = datadir, package = "marray")
}


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### code chunk number 4: RMAGEML.Rnw:128-132
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#To obtain an marrayInfo object containing the database identifiers of the features present on the array.#
data<-system.file("MAGEMLdata", package="RMAGEML")
mageom<-importMAGEOM(directory=data)
getGnames(mageom, arrayID="A-MEXP-14", DED="DED:707", package = "marray")


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### code chunk number 5: RMAGEML.Rnw:140-144
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data<-system.file("MAGEMLdata", package="RMAGEML")
#To obtain an marrayInfo object containing the database identifiers of the features present on the array.#
mageom<-importMAGEOM(directory=data)
getArrayLayout(mageom, arrayID="A-MEXP-14", DED="DED:707")


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### code chunk number 6: RMAGEML.Rnw:151-157
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data<-system.file("MAGEMLdata", package="RMAGEML")
#To obtain an marrayInfo object containing the database identifiers of the features present on the array.#
mageom<-importMAGEOM(directory=data)
gnames<-getGnames(mageom, arrayID="A-MEXP-14", DED = "DED:707", package = "marray")
layout<-getArrayLayout(mageom, arrayID="A-MEXP-14", DED = "DED:707")
raw <- makeMarrayRaw(mageOM=mageom, layout = layout, gnames = gnames, directory = data, arrayID="A-MEXP-14", DED = "DED:707",QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median")


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### code chunk number 7: RMAGEML.Rnw:168-172
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## create RGList object
datadir <- system.file("MAGEMLdata", package="RMAGEML")
raw <- importMAGEML(directory = datadir, package = "limma", arrayID="A-MEXP-14", DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median")
print(raw)


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### code chunk number 8: RMAGEML.Rnw:181-186
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data<-system.file("MAGEMLdata", package="RMAGEML")
#To obtain an marrayInfo object containing the database identifiers of the features present on the array.#
mageom<-importMAGEOM(directory=data)
genes<-getArrayLayoutLimma(mageom, arrayID = "A-MEXP-14", DED="DED:707")
print(genes[1:10,])


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### code chunk number 9: RMAGEML.Rnw:192-197
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data<-system.file("MAGEMLdata", package="RMAGEML")
#To obtain an marrayInfo object containing the database identifiers of the features present on the array.#
mageom<-importMAGEOM(directory=data)
genes<-getArrayLayoutLimma(mageom, arrayID = "A-MEXP-14", DED = "DED:707")
raw<- makeRG(mageOM=mageom, genes = genes, directory=data, arrayID="A-MEXP-14", DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean" ,name.Gb = "QT:B532 Median")