Get exonFrames metadata from makeTranscriptDbFromUCSC command
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Jake ▴ 90
@jake-7236
Last seen 7 months ago
United States

Hi, 

I am trying to make a genomic features object of all consensus CDS exons in the mouse genome from the cCDS table in the UCSC genome browser. I can get this information via

txdb <- makeTranscriptDbFromUCSC(genome="mm10", tablename="ccdsGene")
cds(txdb)

However, the information on the UCSC browser contains a metadata column called exonFrames that I would like to pull down as well. I have looked through the options for makeTranscriptDbFromUCSC and didn't see an obvious way to do this. I was wondering if there is another way?

Thanks

 

 

genomicfeatures genomicranges ucsc • 899 views
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@herve-pages-1542
Last seen 2 days ago
Seattle, WA, United States

Hi Jake,

The bad news is that the "exonFrames" column is ignored by makeTranscriptDbFromUCSC(). The good news is that the frame of each CDS in a given transcript can be inferred from its offset within the transcript, that is, from the cumulated widths of the CDS'es preceding it in the transcript. Here is a function that does it. Like cdsBy(..., by="tx") it returns the CDS'es grouped by transcript but with the additional "frame" inner metadata column:

cdsByTx <- function(txdb, use.names=FALSE)
{
    cds_by_tx <- cdsBy(txdb, by="tx", use.names=use.names)
    offset <- cumsum(width(cds_by_tx))
    offset <- pc(rep.int(0L, length(offset)), phead(offset, n=-1))
    frame <- offset %% 3L
    frame <- as.integer(unlist(frame, use.names=FALSE))
    unlisted_ans <- unlist(cds_by_tx, use.names=FALSE)
    mcols(unlisted_ans)$frame <- frame
    relist(unlisted_ans, cds_by_tx)
}

Then:

library(GenomicFeatures)
txdb <- makeTranscriptDbFromUCSC(genome="mm10", tablename="ccdsGene")

## Note that for the ccdsGene table the reported transcripts are actually CDS
## regions. This means that exons and CDS'es are the same and that there are
## no UTRs:
all(cds(txdb) == exons(txdb))  # TRUE
length(fiveUTRsByTranscript(txdb))  # 0
length(threeUTRsByTranscript(txdb))  # 0

mm10_cds_by_tx <- cdsByTx(txdb, use.names=TRUE)

mm10_cds_by_tx[c(5, 10, 710)]
# GRangesList object of length 3:
# $CCDS14809.1
# GRanges object with 3 ranges and 4 metadata columns:
#       seqnames             ranges strand |    cds_id    cds_name exon_rank
#          <Rle>          <IRanges>  <Rle> | <integer> <character> <integer>
#   [1]     chr1 [5589049, 5589305]      + |        34        <NA>         1
#   [2]     chr1 [5598590, 5598942]      + |        35        <NA>         2
#   [3]     chr1 [5602252, 5602784]      + |        36        <NA>         3
#           frame
#       <integer>
#   [1]         0
#   [2]         2
#   [3]         1
#
# $CCDS14811.1
# GRanges object with 1 range and 4 metadata columns:
#       seqnames             ranges strand | cds_id cds_name exon_rank frame
#   [1]     chr1 [9545524, 9546621]      + |     88     <NA>         1     0
#
# $CCDS48226.1
# GRanges object with 2 ranges and 4 metadata columns:
#       seqnames               ranges strand | cds_id cds_name exon_rank frame
#   [1]     chr1 [18265026, 18265080]      - |   6360     <NA>         1     0
#   [2]     chr1 [18251200, 18251333]      - |   6358     <NA>         2     1
#
# -------
# seqinfo: 66 sequences (1 circular) from mm10 genome

As a sanity check, now we're going to check that our inferred "frame" is the same as the "exonFrames" column found in the ccdsGene table. For this, we're first going to fetch the full table from UCSC using getTable() from the rtracklayer package:

library(rtracklayer)
session <- browserSession()
genome(session) <- "mm10"
query <- ucscTableQuery(session, "CCDS", table="ccdsGene")
mm10_ccdsGene <- getTable(query)
mm10_ccdsGene[c(1,7,70), ]
#    bin        name chrom strand   txStart     txEnd  cdsStart    cdsEnd
# 1    0 CCDS15305.1  chr1      - 134202950 134234355 134202950 134234355
# 7    2 CCDS48344.1  chr1      + 125677336 125872884 125677336 125872884
# 70  76 CCDS14803.1  chr1      -   3216021   3671348   3216021   3671348
#    exonCount               exonStarts                 exonEnds score name2
# 1          2     134202950,134234014,     134203590,134234355,     0    NA
# 7          2     125677336,125872369,     125678192,125872884,     0    NA
# 70         3 3216021,3421701,3670551, 3216968,3421901,3671348,     0    NA
#    cdsStartStat cdsEndStat exonFrames
# 1          cmpl       cmpl       2,0,
# 7          cmpl       cmpl       0,1,
# 70         cmpl       cmpl     1,2,0,

Just a confirmation that for this table the reported transcripts are actually CDS regions:

identical(mm10_ccdsGene[,"txStart"], mm10_ccdsGene[,"cdsStart"])  # TRUE
identical(mm10_ccdsGene[,"txEnd"], mm10_ccdsGene[,"cdsEnd"])  # TRUE

Note that you can use makeGRangesFromDataFrame() to turn mm10_ccdsGene into a GRanges object:

gr <- makeGRangesFromDataFrame(mm10_ccdsGene,
                               start.field="txStart", end.field="txEnd",
                               starts.in.df.are.0based=TRUE,
                               keep.extra.columns=TRUE)

Now let's compare our inferred "frame" with mm10_ccdsGene$exonFrames:

cds_frames <- relist(mcols(unlist(mm10_cds_by_tx, use.names=FALSE))$frame,
                     mm10_cds_by_tx)
cds_frames <- cds_frames[mm10_ccdsGene$name]
cds_frames <- revElements(cds_frames, mm10_ccdsGene$strand == "-")
exonFrames <- IntegerList(strsplit(as.character(mm10_ccdsGene$exonFrames),
                          ",", fixed=TRUE))
identical(unname(cds_frames), exonFrames)  # TRUE

Cheers,

H.

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