Hi, I would like to export the GO annotations to either csv or txt:

1. Go to gene id:

example: GOxxxxxx; gene1,gene2,gene3.....

1. gene id to GO:

example: gene1; GO term1, GO term2, GO term3 .....

I've been trying the following code:

library(org.Pf.plasmo.db)
xgo <- org.Pf.plasmoGO
mapped_genes <- mappedkeys(xgo)
xx2 <- as.list(xgo[mapped_genes])

It produces a complex list with at least 3 levels.

Could you please help advise how to extract these information into a excel sheet?

It would be better if I can also differentiate between GO terms of biological process, cellular components and molecular functions individually, as well as altogether.

Thanks!

Jonas

The first direction:

> go2gn <- sapply(mapIds(org.Pf.plasmo.db, keys(org.Pf.plasmo.db, "GO"), "ORF", "GO", multivals = "list"), paste, collapse = ",")
'select()' returned 1:many mapping between keys and columns

> go2gn.df <- data.frame(GOIDS = names(go2gn), ORF = go2gn)
> head(go2gn.df)
                GOIDS           ORF
GO:0004872 GO:0004872 PF3D7_0100100
GO:0009405 GO:0009405 PF3D7_0100100
GO:0016021 GO:0016021 PF3D7_0100100
GO:0016337 GO:0016337 PF3D7_0100100
GO:0020002 GO:0020002 PF3D7_0100100
GO:0020013 GO:0020013 PF3D7_0100100

## and the reverse

> gn2go <- sapply(mapIds(org.Pf.plasmo.db, keys(org.Pf.plasmo.db), "GO", "ORF", multiVals = "list"), paste, collapse = ",")
'select()' returned 1:many mapping between keys and columns
> gn2go.df <- data.frame(ORF = names(gn2go), GOIDS = gn2go)
> head(gn2go.df)
                        ORF
PF3D7_0100100 PF3D7_0100100
PF3D7_0100200 PF3D7_0100200
PF3D7_0100300 PF3D7_0100300
PF3D7_0100400 PF3D7_0100400
PF3D7_0100500 PF3D7_0100500
PF3D7_0100600 PF3D7_0100600
                                                                                                                      GOIDS
PF3D7_0100100 GO:0004872,GO:0009405,GO:0016021,GO:0016337,GO:0020002,GO:0020013,GO:0020030,GO:0020033,GO:0020035,GO:0050839
PF3D7_0100200                                             GO:0020002,GO:0020003,GO:0020013,GO:0020033,GO:0020035,GO:0020036
PF3D7_0100300                                                                              GO:0004872,GO:0009405,GO:0016021
PF3D7_0100400                                             GO:0020002,GO:0020003,GO:0020013,GO:0020033,GO:0020035,GO:0020036
PF3D7_0100500                                                                                                            NA
PF3D7_0100600                                                                              GO:0016020,GO:0020002,GO:0020033

You can then use e.g., write.xlsx in the openxlsx package to write to an Excel workbook.