Hello,

I have an object with GO numbers (values), and their genes (ind) which is made from the getgo function from goseq:

all23kGos <- stack(getgo(assayed.genes,'hg19','geneSymbol'))

sorted<-all23kGos[order(all23kGos$values),]

> tail(sorted,10)
            values    ind
1755978 GO:2001300 ALOX15
227119  GO:2001301 ALOX12
1755979 GO:2001301 ALOX15
227120  GO:2001302 ALOX12
1755980 GO:2001302 ALOX15
227121  GO:2001303 ALOX12
1755981 GO:2001303 ALOX15
227122  GO:2001304 ALOX12
227123  GO:2001306 ALOX12
895887  GO:2001311   ACP6

Now I would like to print these genes to a tab. delim. txt file, in such a way that every row contains all genes from one GO term separated by tabs. In the end all GO terms have their own row containing all the genes. 

Is this possible with an easy one liner, or do I have to make a complicated for loop for this?

Thanks in advance!

Ben

You can do this using dplyr and grouping by the GO value, e.g.

library(dplyr)
reshaped <- group_by(sorted, values) %>% summarise(genes = paste(ind, collapse = "\t"))
write.table(reshaped, file = "/tmp/tmp.txt", sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)

GO:2001300    ALOX15
GO:2001301    ALOX12    ALOX15
GO:2001302    ALOX12    ALOX15
GO:2001303    ALOX12    ALOX15
GO:2001304    ALOX12
GO:2001306    ALOX12
GO:2001311    ACP6