makePDpackage {makePlatformDesign} | R Documentation |
This function creates the Platform Design package for Affymetrix and NimbleGen chips.
makePDpackage(designFile, file1=NULL, file2=NULL, manufacturer=c("affymetrix", "nimblegen"), type=c("expression", "SNP", "tiling"), extra=NULL)
designFile |
a string with the name of the CDF/NDF file |
file1 |
the FASTA/tab sequence file or the XYS file |
file2 |
the annotation or *.POS file |
manufacturer |
a choice between "affymetrix" or "nimblegen" |
type |
a choice between "expression" or "SNP" |
extra |
a list with several options for customization |
designFile
is either a CDF or an NDF file, depending on the
platform being used.
file1
is the FASTA sequence file if using an Affymetrix SNP
Chip. It will be the tab-delimited sequence file if using an
Affymetrix Expression Chip. If using a NimbleGen Chip, then it is an
XYS file.
file2
is the annotation file for Affymetrix Chips or the *.POS
file for NimbleGen Chips. Required for SNP Chips, optional otherwise.
extra
is a list containing *all* the following elements:
"packagename" (desired package name), "cdf.path" (path to the CDF),
"package.path" (path where the package is to be saved), "author"
(author of the package), "maintainer" (maintainer of the package),
"version" (version of the package), "unlink" (boolean, deletes the
package.path dir if it already exists), "verbose" (boolean).
Either an affysnpBatch
or an affyexprsBatch
object,
depending on the type of the array (SNP or expression).
Benilton Carvalho bcarvalh@jhsph.edu, Rafael A. Irizarry, Ben Bolstad.
## NOT RUN ## ## -- Affymetrix Expression Chip -- ## makePDpackage("CDF", "TAB-sequence-file", manufacturer="affymetrix", ## type="expression") ## ## -- Affymetrix SNP Chip -- ## makePDpackage("CDF", "FASTA", "ANNOT", manufacturer="affymetrix", ## type="SNP") ## ## -- NimbleGen Expression Chip -- ## makePDpackage("NDF", "XYS", "POS", manufacturer="nimblegen", ## type="expression")