Map Genest 1.0 Id To Symbol Using Bioconductor

Question

[brentp]

I want to get the Symbol for probes on the HuGeneSt 1.0 gene array. I can do something like this:

mget(c("8093624"), hugene10sttranscriptclusterSYMBOL)

to get a single probe and see it's what I want. And I can do this:

vals = mget(keys, hugene10sttranscriptclusterSYMBOL)

to get the entire set of mappings. How can I then write vals to a file with columns of ID, SYMBOL?

EDIT: This question is answered, but an addition, what if I wanted the table with an additional column for hugene10sttranscriptclusterGENENAME --where the table will include rows where there's a value for either GENENAME or SYMBOL?

[Martin Morgan]

try toTable(hugene10sttranscriptclusterSYMBOL) for the whole shooting match, or toTable(hugene10sttranscriptclusterSYMBOL[keys]) then standard R.

[boczniak767]

If I understand you correctly - you can use write.table function to save your mappings to external file.

[brentp]

@Martin, thanks, write.table(toTable(hugene10sttranscriptclusterSYMBOL)), "out.tsv", row.names=F, col.names=T, sep="t") works as well.

[brentp]

@Martin, and see my edit to the question.

Answer 1

[Neilfws]

You can convert the list vals to a dataframe using ldply from the plyr package, then use write.table().

library(plyr)
vals <- ldply(vals)
colnames(vals) <- c("ID", "SYMBOL")
write.table(vals, file = "vals.tsv", sep = "\t",
                  col.names = T, row.names = F, quote = F) #tab-separated

[brentp]

great! thanks, I inserted: vals = vals[vals$SYMBOL != NA,]. I'll have a look at plyr.

[brentp]

I added a bit to the question if you care to look.