Identify accepted columns in TxDb objects
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@lluis-revilla-sancho
Last seen 17 hours ago
European Union

How can I know the columns accepted when querying a TxDb object?

I can explore the columns via columns but then other keys are accepted too:

suppressPackageStartupMessages(library("TxDb.Hsapiens.UCSC.hg19.knownGene"))
columns(TxDb.Hsapiens.UCSC.hg19.knownGene)
#>  [1] "CDSCHROM"   "CDSEND"     "CDSID"      "CDSNAME"    "CDSSTART"  
#>  [6] "CDSSTRAND"  "EXONCHROM"  "EXONEND"    "EXONID"     "EXONNAME"  
#> [11] "EXONRANK"   "EXONSTART"  "EXONSTRAND" "GENEID"     "TXCHROM"   
#> [16] "TXEND"      "TXID"       "TXNAME"     "TXSTART"    "TXSTRAND"  
#> [21] "TXTYPE"
genes(TxDb.Hsapiens.UCSC.hg19.knownGene, columns = "GENEID")
#>   403 genes were dropped because they have exons located on both strands
#>   of the same reference sequence or on more than one reference sequence,
#>   so cannot be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a
#>   GRangesList object, or use suppressMessages() to suppress this message.
#> GRanges object with 23056 ranges and 1 metadata column:
#>         seqnames              ranges strand |          GENEID
#>            <Rle>           <IRanges>  <Rle> | <CharacterList>
#>       1    chr19   58858172-58874214      - |               1
#>      10     chr8   18248755-18258723      + |              10
#>     100    chr20   43248163-43280376      - |             100
#>    1000    chr18   25530930-25757445      - |            1000
#>   10000     chr1 243651535-244006886      - |           10000
#>     ...      ...                 ...    ... .             ...
#>    9991     chr9 114979995-115095944      - |            9991
#>    9992    chr21   35736323-35743440      + |            9992
#>    9993    chr22   19023795-19109967      - |            9993
#>    9994     chr6   90539619-90584155      + |            9994
#>    9997    chr22   50961997-50964905      - |            9997
#>   -------
#>   seqinfo: 93 sequences (1 circular) from hg19 genome
genes(TxDb.Hsapiens.UCSC.hg19.knownGene, columns = "gene_id")
#>   403 genes were dropped because they have exons located on both strands
#>   of the same reference sequence or on more than one reference sequence,
#>   so cannot be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a
#>   GRangesList object, or use suppressMessages() to suppress this message.
#> GRanges object with 23056 ranges and 1 metadata column:
#>         seqnames              ranges strand |     gene_id
#>            <Rle>           <IRanges>  <Rle> | <character>
#>       1    chr19   58858172-58874214      - |           1
#>      10     chr8   18248755-18258723      + |          10
#>     100    chr20   43248163-43280376      - |         100
#>    1000    chr18   25530930-25757445      - |        1000
#>   10000     chr1 243651535-244006886      - |       10000
#>     ...      ...                 ...    ... .         ...
#>    9991     chr9 114979995-115095944      - |        9991
#>    9992    chr21   35736323-35743440      + |        9992
#>    9993    chr22   19023795-19109967      - |        9993
#>    9994     chr6   90539619-90584155      + |        9994
#>    9997    chr22   50961997-50964905      - |        9997
#>   -------
#>   seqinfo: 93 sequences (1 circular) from hg19 genome

Created on 2023-01-03 with reprex v2.0.2

I don't know if there is some translation/match between the accepted parameter in the accessors or if there are some hidden columns not provided by columns.
I couldn't find anything documented in ?GenomicFeatures::genes except that in filtere there are some hard coded filter names that seem to be used also for columns (Using Bioconductor version 3.16 with TxDb.Hsapiens.UCSC.hg19.knownGene version 3.2.2).

TxDb • 573 views
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