Annotation the genes for a given Gencode TxDb object

Based on a TxDb object built by gencode_txdb() this function annotates the genes. This information is then used by packages like derfinder and derfinderPlot.

gencode_annotated_genes(txdb)

Arguments

txdb: A GenomicFeatures::TxDb object built with gencode_txdb().

Value

The annotated genes resulting from bumphunter::annotateTranscripts().

References

Based on code for the brainflowprobes package at: https://github.com/LieberInstitute/brainflowprobes/blob/devel/data-raw/create_sysdata.R

Author

Leonardo Collado-Torres.

Examples


## Start from scratch if you want:
if (FALSE) { # \dontrun{
txdb_v31_hg19_chr21 <- gencode_txdb("31", "hg19", chrs = "chr21")
} # }

## or read in the txdb object for hg19 chr21 from this package
txdb_v31_hg19_chr21 <- AnnotationDbi::loadDb(
    system.file("extdata", "txdb_v31_hg19_chr21.sqlite",
        package = "GenomicState"
    )
)
#> Loading required package: GenomicFeatures
#> Loading required package: S4Vectors
#> Loading required package: stats4
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: GenomeInfoDb
#> Loading required package: GenomicRanges
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:AnnotationHub’:
#> 
#>     cache

## Obtain the annotated genes for the Gencode TxDb object
genes_v31_hg19_chr21 <- gencode_annotated_genes(txdb_v31_hg19_chr21)
#> 2024-12-12 22:29:43.929076 annotating the transcripts
#> No annotationPackage supplied. Trying org.Hs.eg.db.
#> Loading required package: org.Hs.eg.db
#> 
#> Getting TSS and TSE.
#> Getting CSS and CSE.
#> Getting exons.
#> Annotating genes.
#> 'select()' returned 1:many mapping between keys and columns

## Explore the result
genes_v31_hg19_chr21
#> GRanges object with 823 ranges and 8 metadata columns:
#>         seqnames            ranges strand |       CSS       CSE
#>            <Rle>         <IRanges>  <Rle> | <integer> <integer>
#>     [1]    chr21 43218385-43299591      - |  43221400  43299480
#>     [2]    chr21 45719934-45747259      + |  45719989  45746745
#>     [3]    chr21 33245333-33416946      + |  33245988  33416425
#>     [4]    chr21 47401651-47424964      + |  47401765  47423927
#>     [5]    chr21 34696734-34732170      + |  34697361  34727855
#>     ...      ...               ...    ... .       ...       ...
#>   [819]    chr21 45188201-45191547      + |      <NA>      <NA>
#>   [820]    chr21 25229397-25261466      + |      <NA>      <NA>
#>   [821]    chr21 38709684-38739160      - |      <NA>      <NA>
#>   [822]    chr21 42108244-42126814      + |      <NA>      <NA>
#>   [823]    chr21 25076577-25081662      + |      <NA>      <NA>
#>                           Tx          Geneid         Gene
#>                  <character>           <Rle>        <Rle>
#>     [1] ENSG00000141956.13_3 ENSG00000141956       PRDM15
#>     [2] ENSG00000141959.17_2 ENSG00000141959         PFKL
#>     [3]  ENSG00000142149.9_4 ENSG00000142149         HUNK
#>     [4] ENSG00000142156.14_2 ENSG00000142156       COL6A1
#>     [5] ENSG00000142166.13_4 ENSG00000142166       IFNAR1
#>     ...                  ...             ...          ...
#>   [819]  ENSG00000287507.1_1 ENSG00000287507         <NA>
#>   [820]  ENSG00000287612.1_1 ENSG00000287612         <NA>
#>   [821]  ENSG00000287637.1_1 ENSG00000287637         <NA>
#>   [822]  ENSG00000288069.1_1 ENSG00000288069         <NA>
#>   [823]  ENSG00000288094.1_1 ENSG00000288094 LOC105372749
#>                         Refseq    Nexons
#>                          <Rle> <integer>
#>     [1] NM_001040424 NM_0012..        32
#>     [2] NM_001002021 NM_0026..        20
#>     [3] NM_014586 NP_055401 ..        12
#>     [4]    NM_001848 NP_001839        35
#>     [5] NM_000629 NM_0013844..        13
#>     ...                    ...       ...
#>   [819]                   <NA>         3
#>   [820]                   <NA>         4
#>   [821]                   <NA>         2
#>   [822]                   <NA>         2
#>   [823] XR_007089952 XR_0070..         3
#>                                                             Exons
#>                                                     <IRangesList>
#>     [1] 43218385-43221882,43222872-43223278,43224694-43224883,...
#>     [2] 45719934-45720073,45724158-45724338,45725077-45725300,...
#>     [3] 33245333-33246248,33296780-33297072,33312477-33312532,...
#>     [4] 47401651-47401861,47402548-47402677,47404183-47404383,...
#>     [5] 34696734-34696943,34697209-34697436,34707830-34707953,...
#>     ...                                                       ...
#>   [819]     45188201-45188277,45189155-45189271,45190985-45191547
#>   [820] 25229397-25229860,25231273-25231484,25233548-25233655,...
#>   [821]                       38709684-38711756,38738974-38739160
#>   [822]                       42108244-42108309,42125644-42126814
#>   [823]     25076577-25076893,25077415-25077672,25080924-25081662
#>   -------
#>   seqinfo: 1 sequence from hg19 genome

Arguments

Value

References

See also

Author

Examples