Question: R org.Hs.eg.db matching ensembl gene ids with gene symbol
0
gravatar for User6891
19 months ago by
User6891190
Europe
User6891190 wrote:

Hi,

I want to add a column with the gene symbol corresponding to the Ensembl Gene ID to a dataframe in R

resOrdered$symbol <- mapIds(org.Hs.eg.db,
                     keys=row.names(resOrdered),
                     column="SYMBOL",
                     keytype="ENSEMBL",
                     multiVals="first")

I'm using 'org.Hs.eg.db' from BioConductor for this. 

I get the following error:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.

I think this is because my row.names from my dataframe resOrdered look like this:

[9997] "ENSG00000100601.5"  "ENSG00000178826.6"  "ENSG00000243663.1"  "ENSG00000138231.8" 

I think the problem is that there are '.', that signify the version, after the actual ENGS. Is there a way to still find a match with the 'ENSEMBL' key from 'org.Hs.eg.db'?

 

 

 

 

bioconductor R • 2.2k views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 19 months ago by User6891190
3

Otherwise, you can always remove the string after the period.

tmp=gsub("\\..*","",row.names(resOrdered)​)
ADD REPLYlink written 19 months ago by Sukhdeep Singh9.0k

hello Sukhdeep,

I have exactly the same question as User6891 and after i try to remove the decimal i get an error.

Error: unexpected input in "tmp=gsub("\..*","",row.names(res)�"

Could you please help me with this?

ADD REPLYlink written 16 months ago by saamar.rajput10
1

Command should work, I see you have some unidentified symbol in the command you pasted. Try to write it and see if it works!

ADD REPLYlink written 16 months ago by Sukhdeep Singh9.0k

tmp=gsub("\..*","",row.names(res)​)

this is my command ...and it shows a question mark in the error.

Error: unexpected input in "tmp=gsub("\..*","",row.names(res)�"

ADD REPLYlink modified 16 months ago • written 16 months ago by saamar.rajput10

As I said, the above command should work, unless you have a copy-paste error, or the object res has some issue. Check row.names(res), what does it outputs!

ADD REPLYlink written 16 months ago by Sukhdeep Singh9.0k

Its working thanks alot :) and thanks for your patience. But 1 more question how do i put the edited ENSEMBL id from tmp back to my res column? I know it is a very basic question but I am new to R.

ADD REPLYlink written 16 months ago by saamar.rajput10

Thanks alot Sukhdeep ...it all worked fine :)

ADD REPLYlink written 16 months ago by saamar.rajput10

Great, good luck then!

ADD REPLYlink written 16 months ago by Sukhdeep Singh9.0k

How did you eventually add tmp back to the res row.names? The answer is not in this thread and I can't figure it out.

Also, is it possible to edit the gene ids in-place instead of creating 'tmp'?

ADD REPLYlink modified 7 days ago • written 7 days ago by Mthabisi Moyo0

can you explain what does it "\\..*","",

ADD REPLYlink written 4 months ago by krushnach80160

remove the string after the period i.e. delete (technically substitute) everything that follows. See this.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax33k
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