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Protein to gene name conversion

I have an R data frame containing peptides in UniProtKB ID format. I used the Uniprot online conversion tool to convert these IDs to gene names. The output is a .txt file with the protein ID in column 1 and gene name in column 2. The issue is that the tool didn't find gene names for all of the protein IDs, so it's not a 1 to 1 list. There may be some peptides that don't have gene names assigned to them.

Examples of the peptide names: 
Q6SPF0
P52701
Q8NAF0
H0Y6H0
P19338
P19338

So, I want to iterate through the column of my peptide list in R and if there is a match in the .txt file, I want to create a new column in my data frame in R and paste the gene name. I would appreciate some help as to how to do this.

Is there a way I could do this all in R rather than having to use the online converter tool?

id r
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updated by GenoMax GenoMax • written by mm2568 • mm2568

Using EntrezDirect:

$ more id.txt
Q6SPF0
P52701
Q8NAF0
P19338

$ for i in `cat id.txt`; do printf ${i}"\t"; esearch -db protein -query ${i} | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name; done
Q6SPF0  SAMD1
P52701  MSH6
Q8NAF0  ZNF579
P19338  NCL

If there is no entry for a particular accession it generates a nasty error. No way around that.

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written by GenoMax GenoMax

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