Subsetting txdb object by "tx_name"
0
0
Entering edit mode
23 months ago
Trivas ★ 1.7k

I've been working on improving the default data visualization of a package by extracting a GRanges object and plotting it using the GViz package. But I can't seem to plot specific isoforms with lines/arrows connecting exons. exonInfo contains the data extracted from a larger R object.

> exonInfo
GRanges object with 640 ranges and 2 metadata columns:
        seqnames              ranges strand |         isoform_id               gene_id
           <Rle>           <IRanges>  <Rle> |        <character>           <character>
    [1]        1 150195168-150195239      + | ENSMUST00000191228 ENSMUSG00000006007.15
    [2]        1 150195168-150195251      + | ENSMUST00000165062 ENSMUSG00000006007.15
    [3]        1 150195177-150195251      + | ENSMUST00000186572 ENSMUSG00000006007.15
    [4]        1 150195180-150195251      + | ENSMUST00000185698 ENSMUSG00000006007.15
    [5]        1 150204067-150204151      + | ENSMUST00000165062 ENSMUSG00000006007.15
    ...      ...                 ...    ... .                ...                   ...
  [636]       18   76435150-76435287      + | ENSMUST00000168423 ENSMUSG00000024563.17
  [637]       18   76435454-76435598      + | ENSMUST00000025453 ENSMUSG00000024563.17
  [638]       18   76435454-76435598      + | ENSMUST00000168423 ENSMUSG00000024563.17
  [639]       18   76437678-76438365      + | ENSMUST00000025453 ENSMUSG00000024563.17
  [640]       18   76437678-76444034      + | ENSMUST00000168423 ENSMUSG00000024563.17
  -------
  seqinfo: 39 sequences from an unspecified genome; no seqlengths

When I plot it as an AnnotationTrack with GViz, I get something that looks like this

exonInfo only

I was a little confused why the introns aren't represented by lines/arrows like when I plot my exonInfo GRanges object alongside my txdb as a GeneRegionTrack.

exonInfo with txdb

So I was hoping to get help doing one of two things:

  1. "correct" my exonInfo GRanges object to include the lines separating introns. I've tried plotting exonInfo as a GeneRegionTrack and it changes the arrows to blocks.
  2. Subset the above txdb object using the isoform ids from exonInfo. I've looked into it and select() doesn't return a GRanges object and I can't seem to subset the results from transcripts()
GRanges R Gviz • 471 views
ADD COMMENT

Login before adding your answer.

Traffic: 1581 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