Question

Convert "chrom:position" to gene name

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3.5 years ago

storm1907 ▴ 30

Hello,

I have the output from statistical test, whic$results

            SetID P.value P.value.Noadj P.value.Internal N.Marker.All   
1         1:69270       1     0.6014744        0.4994083            1   
2         1:69511      NA            NA               NA           NA   
3         1:69761       1     0.6014744        0.4994083            1   
4         1:69897       1     0.5527191        0.4994080            1   
5        1:183937      NA            NA               NA           NA   
6        1:601436       1     0.6488377        0.4994087            1   
7        1:601667       1     0.6488377        0.4994087            1   
8        1:609407       1     0.6488377        0.4994087            1

To make data analysis easier, I would like to add corresponding gene column next to chromosomal position. Is it somehow possible?

Thank you!

gene R • 1.4k views

ADD COMMENT • link updated 3.5 years ago by Ram 44k • written 3.5 years ago by storm1907 ▴ 30

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What have you tried? Search the forum for "chromosome coordinate to gene name" and then search online on how to join data frames on a shared set of columns/look for overlaps between two genomic ranges. That should get you to obtaining the dictionary/lookup dataset you need and then mapping it to the dataset you have.

ADD REPLY • link 3.5 years ago by Ram 44k

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I tried to brutally extract second column and put in in UCSC Genome browser. Looked nice, but the problem is that there is not HGNC name option

ADD REPLY • link 3.5 years ago by storm1907 ▴ 30

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Don't add answers unless you're answering the top level question. Use Add Comment or Add Reply instead. What do you mean by you tried to "brutally extract second column"?

ADD REPLY • link 3.5 years ago by Ram 44k

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if u mean simply add a gene column and if implementation in R seems difficult, simple solution is

Export it to tsv

Add column in excel and save in tsv

Reimport in R

Its not clear from your question!

ADD REPLY • link 3.5 years ago by pbpanigrahi ▴ 430

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I would not recommend adding gene name annotations using Excel. A lot of beginners make errors here that cannot be reversed.

ADD REPLY • link 3.5 years ago by Ram 44k

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Ya agreed. Its risky as gene names get changed like SEP1 to September 1 ;)

If no programming experience then excel is the only saviour.

ADD REPLY • link 3.5 years ago by pbpanigrahi ▴ 430

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I have csv file with above content. Sorry, but which one could be appropriate package to get gene names from chromosomal positions from file in Excel?