Hi!

I have a set of target peaks that I would like to link to promoter regions from the mm10 genome annotation. I retrieve the promoter regions and subset them to standard chromosomes as follows:

library(GenomicRanges)
library(GenomicFeatures)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
promoters <- promoters(TxDb.Mmusculus.UCSC.mm10.knownGene)
promoters <- promoters[seqnames(promoters) %in% paste0("chr", c(1:19, "X", "Y"))]

This gives me the following GenomicRanges object

GRanges object with 142314 ranges and 2 metadata columns:
                       seqnames            ranges strand |     tx_id              tx_name
                          <Rle>         <IRanges>  <Rle> | <integer>          <character>
  ENSMUST00000193812.1     chr1   3071253-3073452      + |         1 ENSMUST00000193812.1
  ENSMUST00000082908.1     chr1   3100016-3102215      + |         2 ENSMUST00000082908.1
  ENSMUST00000192857.1     chr1   3250757-3252956      + |         3 ENSMUST00000192857.1
  ENSMUST00000161581.1     chr1   3464587-3466786      + |         4 ENSMUST00000161581.1
  ENSMUST00000192183.1     chr1   3529795-3531994      + |         5 ENSMUST00000192183.1
                   ...      ...               ...    ... .       ...                  ...
  ENSMUST00000187582.6     chrY 90667426-90669625      - |    142310 ENSMUST00000187582.6
  ENSMUST00000191048.1     chrY 90667426-90669625      - |    142311 ENSMUST00000191048.1
  ENSMUST00000238676.1     chrY 90755268-90757467      - |    142312 ENSMUST00000238676.1
  ENSMUST00000177893.1     chrY 90754622-90756821      - |    142313 ENSMUST00000177893.1
  ENSMUST00000179623.1     chrY 90838978-90841177      - |    142314 ENSMUST00000179623.1
  -------
  seqinfo: 66 sequences (1 circular) from mm10 genome

I would like to simplify it to obtain just a canonical transcript per gene, and include the gene symbol as an extra column in the metadata.

Could you please help me figure out how to do so? Thank you!!

Ensembl makes claims as to canonical transcripts, so we can just believe them, I imagine.

> library(Mus.musculus)
> library(TxDb.Mmusculus.UCSC.mm39.knownGene)
## switch the TxDbs
> TxDb(Mus.musculus) <- TxDb.Mmusculus.UCSC.mm39.knownGene
> z <- promoters(TxDb.Mmusculus.UCSC.mm39.knownGene)
Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 2
  out-of-bound ranges located on
  sequences chr4_JH584295v1_random
  and chr5_JH584296v1_random. Note
  that ranges located on a
  sequence whose length is unknown
  (NA) or on a circular sequence
  are not considered out-of-bound
  (use seqlengths() and
  isCircular() to get the lengths
  and circularity flags of the
  underlying sequences). You can
  use trim() to trim these ranges.
  See ?`trim,GenomicRanges-method`
  for more information.

## easier than how you did it
> z <- keepStandardChromosomes(z, pruning.mode = "coarse")

## Add symbols
> z$symbol <- mapIds(Mus.musculus, names(z), "SYMBOL", "TXNAME")
'select()' returned 1:1 mapping
between keys and columns

## what proportion didn't map?
> sum(is.na(z$symbol))/length(z)
[1] 0.2246602

That gives us the symbols. Now let's get canonical.

> library(biomaRt)
> mart <- useEnsembl("ensembl", "mmusculus_gene_ensembl")
> zz <- getBM(c("ensembl_transcript_id_version", "transcript_is_canonical"), "ensembl_transcript_id_version", names(z), mart)

## <takes nap>
## OK, where was I?
## oh yeah, I remember. Now just canonical
> zzcon <- subset(zz, transcript_is_canonical == 1L)

## subset promoters
> zcon <- z[zzcon[,1]]

## et voila!
> zcon
GRanges object with 57078 ranges and 3 metadata columns:
                       seqnames
                          <Rle>
  ENSMUST00000194081.2     chr1
  ENSMUST00000194393.2     chr1
  ENSMUST00000194605.2     chr1
  ENSMUST00000191703.2     chr1
  ENSMUST00000191467.2     chr1
                   ...      ...
  ENSMUST00000181996.2     chrX
  ENSMUST00000127786.4     chrX
  ENSMUST00020181898.1     chrX
  ENSMUST00020182793.1     chrX
  ENSMUST00000144563.2     chrX
                                    ranges
                                 <IRanges>
  ENSMUST00000194081.2 108342807-108345006
  ENSMUST00000194393.2     6978784-6980983
  ENSMUST00000194605.2     6984783-6986982
  ENSMUST00000191703.2     6997983-7000182
  ENSMUST00000191467.2 108695865-108698064
                   ...                 ...
  ENSMUST00000181996.2 102426576-102428775
  ENSMUST00000127786.4 102526661-102528860
  ENSMUST00020181898.1 102504692-102506891
  ENSMUST00020182793.1 102513203-102515402
  ENSMUST00000144563.2 102569315-102571514
                       strand |
                        <Rle> |
  ENSMUST00000194081.2      + |
  ENSMUST00000194393.2      + |
  ENSMUST00000194605.2      + |
  ENSMUST00000191703.2      + |
  ENSMUST00000191467.2      + |
                   ...    ... .
  ENSMUST00000181996.2      - |
  ENSMUST00000127786.4      - |
  ENSMUST00020181898.1      - |
  ENSMUST00020182793.1      - |
  ENSMUST00000144563.2      - |
                           tx_id
                       <integer>
  ENSMUST00000194081.2      2417
  ENSMUST00000194393.2        75
  ENSMUST00000194605.2        76
  ENSMUST00000191703.2        77
  ENSMUST00000191467.2      2418
                   ...       ...
  ENSMUST00000181996.2    146163
  ENSMUST00000127786.4    146164
  ENSMUST00020181898.1    146166
  ENSMUST00020182793.1    146167
  ENSMUST00000144563.2    146168
                                    tx_name
                                <character>
  ENSMUST00000194081.2 ENSMUST00000194081.2
  ENSMUST00000194393.2 ENSMUST00000194393.2
  ENSMUST00000194605.2 ENSMUST00000194605.2
  ENSMUST00000191703.2 ENSMUST00000191703.2
  ENSMUST00000191467.2 ENSMUST00000191467.2
                   ...                  ...
  ENSMUST00000181996.2 ENSMUST00000181996.2
  ENSMUST00000127786.4 ENSMUST00000127786.4
  ENSMUST00020181898.1 ENSMUST00020181898.1
  ENSMUST00020182793.1 ENSMUST00020182793.1
  ENSMUST00000144563.2 ENSMUST00000144563.2
                            symbol
                       <character>
  ENSMUST00000194081.2        <NA>
  ENSMUST00000194393.2        <NA>
  ENSMUST00000194605.2        <NA>
  ENSMUST00000191703.2        <NA>
  ENSMUST00000191467.2        <NA>
                   ...         ...
  ENSMUST00000181996.2        <NA>
  ENSMUST00000127786.4        Xist
  ENSMUST00020181898.1        <NA>
  ENSMUST00020182793.1        <NA>
  ENSMUST00000144563.2        <NA>
  -------
  seqinfo: 22 sequences (1 circular) from mm39 genome