AffyClariomSPDInfoPkgSeed-class: Class "AffyClariomSPDInfoPkgSeed"

In pdInfoBuilder: Platform Design Information Package Builder

Description

PD Info Package Seed for Affymetrix Clariom S Arrays

Objects from the Class

Objects can be created by calls of the form new("AffyClariomSPDInfoPkgSeed", pgfFile, clfFile, coreMps, transFile, ...).

Slots

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

Methods

chipName

chipName

getGeometry

initialize

makePdInfoPackage

package creator

Examples

showClass("AffyClariomSPDInfoPkgSeed")

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RSQLite
Loading required package: affxparser
Loading required package: oligo
Loading required package: oligoClasses
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'oligoClasses'
Welcome to oligoClasses version 1.38.0
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

================================================================================
Welcome to oligo version 1.40.2
================================================================================
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'pdInfoBuilder'
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Class "AffyClariomSPDInfoPkgSeed" [package "pdInfoBuilder"]

Slots:
                                                                      
Name:        probeFile       transFile         coreMps         fullMps
Class: ScalarCharacter ScalarCharacter ScalarCharacter ScalarCharacter
                                                                      
Name:      extendedMps       geneArray         pgfFile         clfFile
Class: ScalarCharacter         logical ScalarCharacter ScalarCharacter
                                                                      
Name:          version         license          author           email
Class:       character       character       character       character
                                                                      
Name:        biocViews        chipName    manufacturer             url
Class:       character       character       character       character
                                                      
Name:      genomebuild        organism         species
Class:       character       character       character

Extends: 
Class "AffySTPDInfoPkgSeed", directly
Class "AffyGeneric1PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 2
Class "AffymetrixPDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 3
Class "PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 4

pdInfoBuilder documentation built on Nov. 8, 2020, 5:19 p.m.