Add GO IDs of the ancestors for a given vector of GO ids

Description

Add GO IDs of the ancestors for a given vector of GO IDs leveraging GO.db package

Usage

addAncestors(go.ids, ontology = c("bp", "cc", "mf"))

Arguments

Value

A vector of GO IDs containing the input GO IDs with the GO IDs of their ancestors added

Author(s)

Lihua Julie Zhu

Examples

go.ids = cbind(c("GO:0008150", "GO:0005576", "GO:0003674"),
               c("ND", "IDA", "ND"), 
               c("BP", "BP", "BP"), c("1", "1", "1"))
addAncestors(go.ids, ontology="bp")

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(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/addAncestors.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addAncestors
> ### Title: Add GO IDs of the ancestors for a given vector of GO ids
> ### Aliases: addAncestors
> ### Keywords: misc
> 
> ### ** Examples
> 
> go.ids = cbind(c("GO:0008150", "GO:0005576", "GO:0003674"),
+                c("ND", "IDA", "ND"), 
+                c("BP", "BP", "BP"), c("1", "1", "1"))
> addAncestors(go.ids, ontology="bp")
     [,1]         [,2]
[1,] "GO:0003674" "1" 
[2,] "GO:0005576" "1" 
[3,] "GO:0008150" "1" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>