Varriant Annotation-exporting results
0
0
Entering edit mode
6.9 years ago
adakoury • 0

I want to export my variant annotation results to a table and save it in my computer hard drive. I tried this "write.table(mydata, "G:/mydata.txt", sep="\t")" but did not work.

SNP R • 1.5k views
ADD COMMENT
0
Entering edit mode

Could you show a sample from your data ? Also are you about the given location G:/mydata.txt is existing ?

ADD REPLY
0
Entering edit mode

Sorry I did not get the second part of the question " Also are you about the given location G:/mydata.txt is existing ?" I changed to my working directory (K drive) but did not help

> rd <- rowRanges(vcf)
> loc <- locateVariants(rd, txdb, CodingVariants())
'select()' returned many:1 mapping between keys and columns
> head(loc, 20541)
GRanges object with 9619 ranges and 9 metadata columns:
       seqnames               ranges strand   | LOCATION  LOCSTART    LOCEND
          <Rle>            <IRanges>  <Rle>   | <factor> <integer> <integer>
     1   chrA03         [2963, 2963]      -   |   coding       334       334
     2   chrA03         [2977, 2977]      -   |   coding       320       320
     3   chrA03         [2989, 2989]      -   |   coding       308       308
     4   chrA03         [4637, 4637]      -   |   coding       393       393
     5   chrA03         [4681, 4681]      -   |   coding       349       349
  >
     1         6       10747         53290        <NA>                
     2         7       10747         53290        <NA>                
     3         8       10747         53290        <NA>                
     4         9       10748         53293        <NA>                
     5        10       10748         53293        <NA>                
   ...       ...         ...           ...         ...             ...
  9615     20536       13466         68355        <NA>                
  9616     20537       13466         68355        <NA>                
  9617     20538       13466         68355        <NA>                
  9618     20539       13466         68355        <NA>                
  9619     20540       13466         68355        <NA>                
              FOLLOWID
       <CharacterList>
     1                
     2                
     3                
     4                
     5                
   ...             ...
  9615                
  9616                
  9617                
  9618                
  9619                
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

write.table(mydata, file="K:/mydata.txt", sep="\t") Error in is.data.frame(x) : object 'mydata' not found

ADD REPLY
1
Entering edit mode

I was trying to say are you sure about that directory is existing but I made a typo. Anyways, first of all this is not a regular R data frame. It is called Granges object. ( https://www.bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf —> check for more detailed info.).

I found a previous post about similar problem. Actually I think this is what you want.

How To Write Data In A Granges Object To A Bed File.

Give it a try to this link, if you can't solve it. I will help you.

Edit: This is not what you want, but it is similar.

ADD REPLY

Login before adding your answer.

Traffic: 1437 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6