Class ImportPreparer and generic newResources

Description

The ImportPreparer and derived classes are used for dispatch during data discovery (see newResources). There is one ImportPreparer class for each data source for AnnotationHubMetadata.

newResources is a generic function; with methods implemented for each ImportPreparer.

Author(s)

Martin Morgan

See Also

AnnotationHubMetadata.

Examples

getImportPreparerClasses()

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(AnnotationHubData)
Loading required package: S4Vectors
Loading required package: stats4
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: AnnotationHub
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AnnotationHubData/ImportPreparer-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ImportPreparer-class
> ### Title: Class 'ImportPreparer' and generic 'newResources'
> ### Aliases: newResources getImportPreparer ImportPreparer-class
> ###   show,ImportPreparer-method newResources,ImportPreparer-method
> ###   UCSCTrackImportPreparer-class UCSCTrackImportPreparer
> ###   newResources,UCSCTrackImportPreparer-method
> ###   newResources,UCSCFullTrackImportPreparer-method
> ###   HaemCodeImportPreparer-class HaemCodeImportPreparer
> ###   newResources,HaemCodeImportPreparer-method EncodeImportPreparer-class
> ###   EncodeImportPreparer newResources,EncodeImportPreparer-method
> ###   annotationHubRoot metadataList metadataTable sourceUrls
> ###   EnsemblFastaImportPreparer-class EnsemblFastaImportPreparer
> ###   newResources,EnsemblFastaImportPreparer-method
> ###   EnsemblGtfImportPreparer-class EnsemblGtfImportPreparer
> ###   newResources,EnsemblGtfImportPreparer-method
> ###   RefNetImportPreparer-class RefNetImportPreparer
> ###   newResources,RefNetImportPreparer-method dbSNPVCFImportPreparer-class
> ###   dbSNPVCFImportPreparer newResources,dbSNPVCFImportPreparer-method
> ###   Grasp2ImportPreparer-class Grasp2ImportPreparer
> ###   newResources,Grasp2ImportPreparer-method
> ###   Inparanoid8ImportPreparer-class Inparanoid8ImportPreparer
> ###   newResources,Inparanoid8ImportPreparer-method
> ###   NCBIImportPreparer-class NCBIImportPreparer
> ###   newResources,NCBIImportPreparer-method UCSCChainPreparer-class
> ###   UCSCChainPreparer newResources,UCSCChainPreparer-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> getImportPreparerClasses()
 [1] "BioPaxImportPreparer"            "ChEAImportPreparer"             
 [3] "dbSNPVCFPreparer"                "EncodeImportPreparer"           
 [5] "EnsemblGtfImportPreparer"        "EnsemblFastaImportPreparer"     
 [7] "EpigenomeRoadMapPreparer"        "GencodeFastaImportPreparer"     
 [9] "GencodeGffImportPreparer"        "Grasp2ImportPreparer"           
[11] "GSE62944ToExpressionSetPreparer" "HaemCodeImportPreparer"         
[13] "Inparanoid8ImportPreparer"       "NCBIImportPreparer"             
[15] "OrgDbFromPkgsImportPreparer"     "PazarImportPreparer"            
[17] "RefNetImportPreparer"            "UCSCChainPreparer"              
[19] "UCSC2BitPreparer"                "UCSCTrackImportPreparer"        
[21] "EnsemblTwoBitPreparer"          
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>