Contructor for annotation object

Description

This function creates the necessary annotation object of class ipDataSource containing the pathway and InterPro ID mappings.

Usage

dataSource(mapping, type = "generic")

Arguments

Details

For genes without pathway membership, NA list items need to be included in mapping. The names of the list comprise the gene universe to test against. The function will access the ensembl biomaRt database in order to retrieve the necessary InterPro domain information.

Value

Object of class ipDataSource

Author(s)

Florian Hahne

See Also

gseDomain, getKEGGdata

Examples

if(interactive())
{
grouping <- list("653361"=c("pw1", "pw2"), "729230"="pw1",
                 "415117"="pw3") 
dataSource(grouping)
}

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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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(domainsignatures)
Loading required package: KEGG.db
Loading required package: AnnotationDbi
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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums


KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: prada
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

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

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.3-11)

Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/domainsignatures/dataSource.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dataSource
> ### Title: Contructor for annotation object
> ### Aliases: dataSource
> ### Keywords: IO
> 
> ### ** Examples
> 
> #if(interactive())
> #{
> grouping <- list("653361"=c("pw1", "pw2"), "729230"="pw1",
+                  "415117"="pw3") 
> dataSource(grouping)
Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.
Calls: dataSource ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted