Functions to transformconvert objects between different types

Description

These functions transform data from one classtype into another, or pack simple processes such as compute the profiles needed for one annotations package.

Usage

as.GOTerms.frame(myGOTermsList, na.rm=TRUE)
as.GOTerms.list(genelist, probeType, orgPackage=NULL, anotPkg=NULL, onto="any", na.rm=TRUE)
BioCpack2EntrezIDS(anotPkg, na.rm=TRUE)
BioCpack2Profiles(anotPkg, orgPackage, level=2, na.rm=TRUE, expanded=FALSE)
BioCprobes2Entrez(probeslist , anotPkg, na.rm=TRUE)
GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)

Arguments

Details

Not yet available

Value

Every function returns a transformed object or a list of computed profiles

Author(s)

Alex Sanchez

Examples

data(CD4Ids)
myGOTermsList <- GOTermsList(CD4LLids[1:5], orgPkg="org.Hs.eg.db")
myGOTermsFrame<- as.GOTerms.frame(myGOTermsList, na.rm=TRUE)
GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(goProfiles)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: AnnotationDbi
Loading required package: stats4
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

Loading required package: GO.db

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/goProfiles/conversionFunctions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: conversionFunctions
> ### Title: Functions to transformconvert objects between different types
> ### Aliases: as.GOTerms.frame as.GOTerms.list BioCpack2EntrezIDS
> ###   BioCpack2Profiles BioCprobes2Entrez GOTermsFrame2GOTermsList
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(CD4Ids)
> myGOTermsList <- GOTermsList(CD4LLids[1:5], orgPkg="org.Hs.eg.db")

> myGOTermsFrame<- as.GOTerms.frame(myGOTermsList, na.rm=TRUE)
> GOTermsFrame2GOTermsList(myGOTermsFrame, evid=FALSE)
$`10160`
          BP           BP           BP           BP           BP           BP 
"GO:0007416" "GO:0010923" "GO:0035023" "GO:0043547" "GO:0043547" "GO:0043547" 
          BP           CC           CC           CC           CC           CC 
"GO:0048813" "GO:0005737" "GO:0005829" "GO:0005856" "GO:0030054" "GO:0030175" 
          CC           CC           CC           MF           MF           MF 
"GO:0030425" "GO:0031234" "GO:0043197" "GO:0005089" "GO:0008092" "GO:0030676" 

$`10461`
          BP           BP           BP           BP           BP           BP 
"GO:0001779" "GO:0006468" "GO:0006909" "GO:0007166" "GO:0007267" "GO:0007283" 
          BP           BP           BP           BP           BP           BP 
"GO:0007596" "GO:0018108" "GO:0018108" "GO:0030168" "GO:0032940" "GO:0034446" 
          BP           BP           BP           BP           BP           BP 
"GO:0043277" "GO:0043491" "GO:0050766" "GO:0050900" "GO:0051250" "GO:0060041" 
          BP           BP           CC           CC           CC           CC 
"GO:0060068" "GO:2000107" "GO:0001750" "GO:0005615" "GO:0005737" "GO:0005886" 
          CC           CC           MF           MF           MF 
"GO:0005887" "GO:0016028" "GO:0004714" "GO:0005515" "GO:0005524" 

$`10579`
          BP           BP           BP           BP           BP           BP 
"GO:0000226" "GO:0008283" "GO:0021987" "GO:0022008" "GO:0022027" "GO:0030953" 
          BP           CC           CC           CC           CC           CC 
"GO:0032886" "GO:0005634" "GO:0005730" "GO:0005737" "GO:0005815" "GO:0015630" 
          MF           MF 
"GO:0019904" "GO:0035257" 

$`10611`
          BP           BP           BP           CC           CC           CC 
"GO:0051963" "GO:0061001" "GO:0061049" "GO:0005829" "GO:0014069" "GO:0015629" 
          CC           CC           CC           CC           CC           MF 
"GO:0016020" "GO:0030018" "GO:0030054" "GO:0043005" "GO:0045211" "GO:0003779" 
          MF           MF           MF           MF           MF 
"GO:0005080" "GO:0005515" "GO:0008270" "GO:0042805" "GO:0047485" 

$`10629`
          BP           BP           BP           BP           BP           BP 
"GO:0006325" "GO:0006338" "GO:0006352" "GO:0006357" "GO:0043966" "GO:0051090" 
          CC           CC           CC           MF           MF           MF 
"GO:0000118" "GO:0030914" "GO:0070062" "GO:0003677" "GO:0003713" "GO:0004402" 
          MF           MF 
"GO:0005515" "GO:0046982" 

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>