getKEGGdata: Fetch KEGG annotations and InterPro domains

In domainsignatures: Geneset enrichment based on InterPro domain signatures

Description

Get all available KEGG annotations and InterPro domains for a set of entrezgene identifiers from the KEGG annotation package and from the ensembl biomaRt.

Usage

getKEGGdata(universe=NULL, pathways=NULL, ensemblMart="hsapiens_gene_ensembl")

Arguments

universe	Character vector of entrezgene identifiers. This is the global universe of genes to test against.
pathways	Optional character vector of KEGG pathway identifiers. This can be used in order to test for over-representation of only a subset of all the available KEGG pathways.
ensemblMart	Character giving the type of Biomart to use. Defaults to Human Ensembl.

Details

This function is a wrapper around the KEGG annotation package and a customized query of the ensembl biomaRt database. For the gene identifiers in universe and all or a selection of KEGG pathways it will fetch the necessary information and create an object of class ipDataSource which can later be used as input to gseDomain

Value

An object of class ipDataSource.

Author(s)

Florian Hahne

See Also

gseDomain

Examples

if(interactive())
getKEGGdata()

Example output

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, 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

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 object is masked from 'package:base':

    expand.grid


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 1.4-4)

Loading required package: biomaRt

domainsignatures documentation built on May 2, 2018, 4:17 a.m.