Title: | Platform Design Information Package Builder |
---|---|
Description: | Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. |
Authors: | Seth Falcon, Vince Carey, Matt Settles, Kristof de Beuf, Benilton Carvalho |
Maintainer: | Benilton Carvalho <[email protected]> |
License: | Artistic-2.0 |
Version: | 1.71.0 |
Built: | 2024-11-18 03:40:26 UTC |
Source: | https://github.com/bioc/pdInfoBuilder |
PD Info Package Seed for Affymetrix Clariom S Arrays
Objects can be created by calls of the form
new("AffyClariomSPDInfoPkgSeed", pgfFile, clfFile, coreMps, transFile, ...)
.
pgfFile
:PGF filename
clfFile
:CLF filename
coreMps
:MPS filename
transFile
:Transcript annotation CSV file
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
chipName
initialize
package creator
showClass("AffyClariomSPDInfoPkgSeed")
showClass("AffyClariomSPDInfoPkgSeed")
PD Info Package Seed for Affymetrix Expression Arrays
Objects can be created by calls of the form new("AffyExpressionPDInfoPkgSeed", cdfFile, csvAnnoFile, tabSeqFile, ...)
.
cdfFile
:CDF filename
celFile
:CEL filename
tabSeqFile
:TAB sequence file
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
chipName
initialize
package creator
showClass("AffyExpressionPDInfoPkgSeed")
showClass("AffyExpressionPDInfoPkgSeed")
This class represents Platform Design (PD) packages for Affymetrix genomewide (SNP 5.0 and SNP 6.0) arrays.
Objects can be created by calls of the form new("AffySNPCNVPDInfoPkgSeed", cdfFile, csvAnnoFile, csvSeqFile, csvAnnoFileCnv, csvSeqFileCnv, splineParamFile, crlmmInfoFile, referenceDistFile, ...)
.
cdfFile
:Path to the CDF file for this.
csvAnnoFile
:Path to the Affymetrix CSV annotation for the SNP probes.
csvSeqFile
:Path to the (SNP) probe sequence file.
csvAnnoFileCnv
:Path to the Affymetrix CSV annotation for the CNV probes.
csvSeqFileCnv
:Path to the (CNV) probe sequence file.
splineParamFile
:Path to the spline parameters file used to
compute the predicted accuracy of the the genotype calls. Used
internally in .predictAccuracy
.
crlmmInfoFile
:Path to is data file containing regions data
used by the crlmm
function.
referenceDistFile
:Path to a reference distribution file used
in the normalization step. This is the reference used in snprma
.
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(object = "AffySNPCNVPDInfoPkgSeed")
: ...
signature(object = "AffySNPCNVPDInfoPkgSeed")
: ...
signature(object = "AffySNPCNVPDInfoPkgSeed")
: ...
*IMPORTANT* Users are strongly advised to download Affymetrix SNP packages from BioConductor.
The files used for slots splineParamFile
, crlmmInfoFile
,
and referenceDistFile
are generated by the Bioconductor project
for each chip/platform and are hosted in our svn data repository at
https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store.
When makePdInfoPackage
is run, these files are simply copied to
the inst/extdata
directory of the generated package.
Benilton Carvalho
showClass("AffySNPCNVPDInfoPkgSeed")
showClass("AffySNPCNVPDInfoPkgSeed")
A generic annotation package builder for Affymetrix SNP/CNV
arrays. This is a simplified version of the annotation package and
crlmm
will *NOT* work for them.
Objects can be created by calls of the form new("AffySNPCNVPDInfoPkgSeed2", csvAnnoFileCnv, csvSeqFileCnv, ...)
.
cdfFile
:Path to the CDF file for this.
csvAnnoFile
:Path to the Affymetrix CSV annotation for the SNP probes.
csvSeqFile
:Path to the (SNP) probe sequence file.
csvAnnoFileCnv
:Path to the Affymetrix CSV annotation for the CNV probes.
csvSeqFileCnv
:Path to the (CNV) probe sequence file.
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(object = "AffySNPCNVPDInfoPkgSeed2")
: ...
signature(object = "AffySNPCNVPDInfoPkgSeed2")
: ...
This is a simplified annotation package. CRLMM won't work for these objects.
The user may need to rename the columns or even add column names to the annotation and sequence files. In case problems are found, column names are suggested.
Benilton Carvalho
showClass("AffySNPCNVPDInfoPkgSeed2")
showClass("AffySNPCNVPDInfoPkgSeed2")
This class represents Platform Design (PD) packages for Affymetrix mapping (SNP chip) arrays.
Objects can be created by calls of the form new("AffySNPPDInfoPkgSeed", splineParamFile, crlmmInfoFile, referenceDistFile, ...)
.
splineParamFile
:Spline parameters file used to compute the predicted accuracy of the genotype calls.
crlmmInfoFile
:Data file containing regions data used
by the crlmm
function.
referenceDistFile
:Reference distribution file used in
the normalization step by snprma
.
cdfFile
:CDF file for the design.
csvAnnoFile
:Affymetrix CSV Annotation file.
csvSeqFile
:Affymetrix Probe Sequence file.
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(object = "AffySNPPDInfoPkgSeed")
: ...
signature(object = "AffySNPPDInfoPkgSeed")
: ...
signature(object = "AffySNPPDInfoPkgSeed")
: ...
*IMPORTANT* The user is strongly advised to download Affymetrix SNP packages from BioConductor.
The files used for slots splineParamFile
, crlmmInfoFile
,
and referenceDistFile
are generated by the Bioconductor project
for each chip/platform and are hosted in our svn data repository at
https://hedgehog.fhcrc.org/bioc-data/trunk/annotation/parms_store.
When makePdInfoPackage
is run, these files are simply copied to
the inst/extdata
directory of the generated package.
showClass("AffySNPPDInfoPkgSeed") cdfFile <- "Mapping250K_Nsp.cdf" csvAnno <- "Mapping250K_Nsp_annot.csv" csvSeq <- "Mapping250K_Nsp_probe_tab" spline <- "pd.mapping250k.nsp.spline.params.rda" refd <- "pd.mapping250k.nspRef.rda" crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda" pkg <- new("AffySNPPDInfoPkgSeed", version="0.1.5", author="A. U. Thor", email="[email protected]", biocViews="AnnotationData", genomebuild="NCBI Build 35, May 2004", cdfFile=cdfFile, csvAnnoFile=csvAnno, csvSeqFile=csvSeq, splineParamFile=spline, crlmmInfoFile=crlmmInf, referenceDistFile=refd) showMethods(classes=class(pkg))
showClass("AffySNPPDInfoPkgSeed") cdfFile <- "Mapping250K_Nsp.cdf" csvAnno <- "Mapping250K_Nsp_annot.csv" csvSeq <- "Mapping250K_Nsp_probe_tab" spline <- "pd.mapping250k.nsp.spline.params.rda" refd <- "pd.mapping250k.nspRef.rda" crlmmInf <- "pd.mapping250k.nspCrlmmInfo.rda" pkg <- new("AffySNPPDInfoPkgSeed", version="0.1.5", author="A. U. Thor", email="[email protected]", biocViews="AnnotationData", genomebuild="NCBI Build 35, May 2004", cdfFile=cdfFile, csvAnnoFile=csvAnno, csvSeqFile=csvSeq, splineParamFile=spline, crlmmInfoFile=crlmmInf, referenceDistFile=refd) showMethods(classes=class(pkg))
A generic annotation package builder for Affymetrix SNP
arrays. This is a simplified version of the annotation package and
crlmm
will *not* work for them.
Objects can be created by calls of the form new("AffySNPPDInfoPkgSeed2", cdfFile, csvAnnoFile, csvSeqFile, ...)
.
axiom
:Logical flag for experimental build of annotation packages for Axiom arrays.
cdfFile
:CDF file for the design.
csvAnnoFile
:Affymetrix CSV Annotation file.
csvSeqFile
:Affymetrix Probe Sequence file.
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(object = "AffySNPPDInfoPkgSeed2")
: ...
This is a simplified annotation package. CRLMM won't work for these objects.
The user may need to rename the columns or even add column names to the annotation and sequence files. In case problems are found, column names are suggested.
showClass("AffySNPPDInfoPkgSeed2")
showClass("AffySNPPDInfoPkgSeed2")
container for parameters related to pdmapping package construction for ST type arrays
Objects can be created by calls of the form new("AffySTPDInfoPkgSeed", pgfFile, clfFile, probeFile, transFile, ...)
.
pgfFile
:Object of class "ScalarCharacter"
path to pgf
clfFile
:Object of class "ScalarCharacter"
path to clf
probeFile
:Object of class "ScalarCharacter"
, path to probe sequence file (Optional)
transFile
:Object of class "ScalarCharacter"
, path to trans file (Optional)
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(object = "AffySTPDInfoPkgSeed")
: ...
signature(object = "AffySTPDInfoPkgSeed")
: ...
signature(object = "AffySTPDInfoPkgSeed")
: ...
B. Carvalho
showClass("AffySTPDInfoPkgSeed")
showClass("AffySTPDInfoPkgSeed")
PD Info Package Seed for Affymetrix Tiling Arrays
Objects can be created by calls of the form new("AffyTilingPDInfoPkgSeed", ...)
.
bpmapFile
:BPMAP File - provided by Affymetrix
celFile
:CEL File - provided by Affymetrix
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(object = "AffyTilingPDInfoPkgSeed")
: ...
signature(object = "AffyTilingPDInfoPkgSeed")
: ...
showClass("AffyTilingPDInfoPkgSeed")
showClass("AffyTilingPDInfoPkgSeed")
Helper functions to assist the creation of an annotation package for a generic array. This includes converting CDF files into flat tables and parsing probe sequence files.
cdf2table(cdfFile) sequenceParser(seqFile)
cdf2table(cdfFile) sequenceParser(seqFile)
cdfFile |
name of the CDF file to be used |
seqFile |
name of the probe sequence file |
cdf2table
will convert a CDF to a flat table.
seqFile
will extract a flat table containing physical location and probe sequences.
This generic function returns an official or standard chip/platform name.
chipName(object)
chipName(object)
object |
See |
The idea is that the input files can be used to determine a standard
name for each platform. For example, the method for
AffySNPPDInfoPkgSeed
objects reads the header of the CDF file
to extract a name.
A character vector of length one giving a standard name for the platform.
Seth Falcon
This generic function returns the geometry for a chip/platform.
getGeometry(object)
getGeometry(object)
object |
See |
The idea is that the input files can be used to determine the
geometry for each platform. For example, the method for
AffySNPPDInfoPkgSeed
objects reads the header of the CDF file
to extract the geometry.
A list with two elements nrows and ncols
Matt Settles
This generic function create a platform design info package based on
the parameters contained in object
which will generally be an
instance of a subclass of PkgSeed
. The result is a new
directory on the filesystem containing the source for the generated
pdInfo package.
makePdInfoPackage(object, destDir, batch_size = 10000, quiet = FALSE, unlink = FALSE)
makePdInfoPackage(object, destDir, batch_size = 10000, quiet = FALSE, unlink = FALSE)
object |
See |
destDir |
Path where the resulting pdInfo package source directory will be written. |
batch_size |
An integer controlling the size of batches
processed when reading the flatfiles and loading the DB. In
general, larger
values of |
quiet |
A logical value. When |
unlink |
A logical value. If 'TRUE', and 'destDir' already contains a file or directory with the name 'pkgname', try to unlink (remove) it. |
In general, creating the SQLite database will be a time and memory intensive task.
This function is called for its side-effect of producing a pdInfo source package directory.
Seth Falcon
cdfFile <- "Mapping250K_Nsp.cdf" csvAnno <- "Mapping250K_Nsp_annot.csv" csvSeq <- "Mapping250K_Nsp_probe_tab" ## Not run: pkg <- new("AffySNPPDInfoPkgSeed", version="0.1.5", author="A.U. Thor", email="[email protected]", biocViews="AnnotationData", genomebuild="NCBI Build 35, May 2004", cdfFile=cdfFile, csvAnnoFile=csvAnno, csvSeqFile=csvSeq) makePdInfoPackage(pkg, destDir=".") ## End(Not run)
cdfFile <- "Mapping250K_Nsp.cdf" csvAnno <- "Mapping250K_Nsp_annot.csv" csvSeq <- "Mapping250K_Nsp_probe_tab" ## Not run: pkg <- new("AffySNPPDInfoPkgSeed", version="0.1.5", author="A.U. Thor", email="[email protected]", biocViews="AnnotationData", genomebuild="NCBI Build 35, May 2004", cdfFile=cdfFile, csvAnnoFile=csvAnno, csvSeqFile=csvSeq) makePdInfoPackage(pkg, destDir=".") ## End(Not run)
PDInfo package Seed for NimbleGen Expression arrays
Objects can be created by calls of the form new("NgsExpressionPDInfoPkgSeed", ndfFile, pairFile, xysFile, ngdFile ...)
.
ndfFile
:NDF (NimbleGen Design) file
xysFile
:XYS File - used as template
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(.Object = "NgsExpressionPDInfoPkgSeed")
: ...
signature(object = "NimbleGenPDInfoPkgSeed")
: ...
signature(.Object = "NimbleGenPDInfoPkgSeed")
: ...
showClass("NgsExpressionPDInfoPkgSeed")
showClass("NgsExpressionPDInfoPkgSeed")
PDInfo package Seed for NimbleGen Tiling arrays
Objects can be created by calls of the form new("NgsTilingPDInfoPkgSeed", ndfFile, xysFile, pairFile, posFile ...)
.
ndfFile
:NDF (NimbleGen Design) file
xysFile
:XYS File - used as template
posFile
:POS (Positions) file
chipName
:Name of the chip or platform
manufacturer
:chip/platform manufacturer
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(.Object = "NgsTilingPDInfoPkgSeed")
: ...
signature(object = "NimbleGenPDInfoPkgSeed")
: ...
signature(object = "NimbleGenPDInfoPkgSeed")
: ...
showClass("NgsTilingPDInfoPkgSeed")
showClass("NgsTilingPDInfoPkgSeed")
PDInfo package Seed for all NimbleGen arrays
Objects can be created by calls of the form new("NimbleGenPDInfoPkgSeed", ...)
.
manufacturer
:Manufacturer = NimbleGen
chipName
:Name of the chip or platform
url
:chip URL
genomebuild
:The genome build this platform is based upon.
organism
:organism for chip.
species
:species for chip.
version
:A character vector giving the version number of the package.
license
:The license of the package
author
:Author of the package
email
:An email address to use in the Maintainer field
biocViews
:Character data for the biocViews field of the DESCRIPTION file
signature(object = "NimbleGenPDInfoPkgSeed")
: ...
signature(object = "NimbleGenPDInfoPkgSeed")
: ...
showClass("NimbleGenPDInfoPkgSeed")
showClass("NimbleGenPDInfoPkgSeed")