Convert "chrom:position" to gene name
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!
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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.
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
Don't add answers unless you're answering the top level question. Use
Add CommentorAdd Replyinstead. What do you mean by you tried to "brutally extract second column"?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!
I would not recommend adding gene name annotations using Excel. A lot of beginners make errors here that cannot be reversed.
Ya agreed. Its risky as gene names get changed like SEP1 to September 1 ;)
If no programming experience then excel is the only saviour.
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?
Please search the forum - there are multiple posts on this topic.