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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).