genWegoFile: Function to generate a format in Wego native style from a...
In PloGO2: Plot Gene Ontology and KEGG pathway Annotation and Abundance

Description Usage Arguments Value Author(s) Examples

Connects to the Uniprot Biomart using functionality from the biomaRt package, downloads GO information and organizes it as needed.

1	genWegoFile(IDList, fname = "Wego.txt", database = "uniprot", outFolder=tempdir())

`IDList`	A list of ID's, either Ensembl or Uniprot.
`fname`	The name of the text file to be outputed.
`database`	`"ensembl"` or `"uniprot"`.
`outFolder`	The output files folder

File path of generated Wego files

D. Pascovici

1
2
3

v <- c("Q9HWC9","Q9HWD0","Q9I4N8","Q9HW18","Q9HWC9","Q9HWD0")

## Not run: genWegoFile(v, fname = "F1.txt")

Loading required package: GO.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’:

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


Loading required package: GOstats
Loading required package: Category
Loading required package: Matrix

Attaching package: ‘Matrix’

The following object is masked from ‘package:S4Vectors’:

    expand

Loading required package: graph

Attaching package: ‘GOstats’

The following object is masked from ‘package:AnnotationDbi’:

    makeGOGraph