genWegoFile: Function to generate a format in Wego native style from a...

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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

Arguments

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

Value

File path of generated Wego files

Author(s)

D. Pascovici

Examples

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3
v <- c("Q9HWC9","Q9HWD0","Q9I4N8","Q9HW18","Q9HWC9","Q9HWD0")

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

Example output

Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

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

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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:S4VectorsThe following object is masked frompackage:base:

    expand.grid


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

Attaching package:MatrixThe following object is masked frompackage:S4Vectors:

    expand

Loading required package: graph

Attaching package:GOstatsThe following object is masked frompackage:AnnotationDbi:

    makeGOGraph

PloGO2 documentation built on Nov. 8, 2020, 5:40 p.m.