TxDb, GenomicFeatures load from GTF file (Mmul_8)
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Entering edit mode
Brian Smith ▴ 120
@brian-smith-6197
Last seen 20 months ago
United States

Hi,

I wanted to get the gene coordinates for Mmul8.0.1, and download the file from ensembl (ftp://ftp.ensembl.org/pub/release-97/gtf/macacamulatta/Macacamulatta.Mmul8.0.1.97.chr.gtf.gz).

When I load the package to txdb object using GenomicFeatures, I don't seem to be getting the genes. The transcripts, cds appears to be ok, but not genes. What am I doing wrong?

thanks for your help!

> library(GenomicFeatures)
> txdbmm <- makeTxDbFromGFF(file = paste0(mmdir,'Macaca_mulatta.Mmul_8.0.1.97.chr.gtf'))

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type stop_codon. This information was ignored.
> seqlevelsStyle(txdbmm) <- "UCSC"

> xx <- transcripts(txdbmm)
> yy <- cds(txdbmm) 
> zz <- genes(txdbmm)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'genes' for signature '"TxDb"'

> txdbmm
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: /Users/Mmul_8.0.1/Macaca_mulatta.Mmul_8.0.1.97.chr.gtf
# Organism: NA
# Taxonomy ID: NA
# miRBase build ID: NA
# Genome: NA
# Nb of transcripts: 55075
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2020-07-11 15:51:11 -0400 (Sat, 11 Jul 2020)
# GenomicFeatures version at creation time: 1.40.1
# RSQLite version at creation time: 2.2.0
# DBSCHEMAVERSION: 1.2

My sessionInfo() is:

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] circlize_0.4.10                      annotatr_1.14.0                      dplyr_1.0.0                         
 [4] regioneR_1.20.1                      Gviz_1.32.0                          org.Mmu.eg.db_3.11.4                
 [7] pvclust_2.2-0                        zoo_1.8-8                            data.table_1.12.8                   
[10] foreign_0.8-80                       gtools_3.8.2                         BSgenome.Hsapiens.UCSC.hg38_1.4.3   
[13] BSgenome.Mmulatta.UCSC.rheMac8_1.4.2 BSgenome_1.56.0                      rtracklayer_1.47.0                  
[16] Biostrings_2.56.0                    XVector_0.28.0                       biomaRt_2.44.1                      
[19] topGO_2.40.0                         SparseM_1.78                         GO.db_3.11.4                        
[22] graph_1.66.0                         org.Hs.eg.db_3.11.4                  reutils_0.2.3                       
[25] XML_3.99-0.4                         DSS_2.36.0                           BiocParallel_1.22.0                 
[28] bsseq_1.24.4                         SummarizedExperiment_1.18.2          DelayedArray_0.14.0                 
[31] matrixStats_0.56.0                   GenomicFeatures_1.40.1               AnnotationDbi_1.50.1                
[34] Biobase_2.48.0                       GenomicRanges_1.40.0                 GenomeInfoDb_1.24.2                 
[37] IRanges_2.22.2                       S4Vectors_0.26.1                     BiocGenerics_0.34.0                 

loaded via a namespace (and not attached):
  [1] backports_1.1.8               Hmisc_4.4-0                   AnnotationHub_2.20.0          BiocFileCache_1.12.0         
  [5] plyr_1.8.6                    lazyeval_0.2.2                splines_4.0.2                 ggplot2_3.3.2                
  [9] digest_0.6.25                 ensembldb_2.12.1              htmltools_0.5.0               magrittr_1.5                 
 [13] checkmate_2.0.0               memoise_1.1.0                 cluster_2.1.0                 limma_3.44.3                 
 [17] readr_1.3.1                   R.utils_2.9.2                 askpass_1.1                   prettyunits_1.1.1            
 [21] jpeg_0.1-8.1                  colorspace_1.4-1              blob_1.2.1                    rappdirs_0.3.1               
 [25] xfun_0.15                     crayon_1.3.4                  RCurl_1.98-1.2                survival_3.2-3               
 [29] VariantAnnotation_1.34.0      glue_1.4.1                    gtable_0.3.0                  zlibbioc_1.34.0              
 [33] Rhdf5lib_1.10.1               shape_1.4.4                   HDF5Array_1.16.1              scales_1.1.1                 
 [37] DBI_1.1.0                     Rcpp_1.0.5                    xtable_1.8-4                  progress_1.2.2               
 [41] htmlTable_2.0.1               bit_1.1-15.2                  Formula_1.2-3                 htmlwidgets_1.5.1            
 [45] httr_1.4.1                    RColorBrewer_1.1-2            acepack_1.4.1                 ellipsis_0.3.1               
 [49] pkgconfig_2.0.3               R.methodsS3_1.8.0             nnet_7.3-14                   dbplyr_1.4.4                 
 [53] locfit_1.5-9.4                reshape2_1.4.4                tidyselect_1.1.0              rlang_0.4.6                  
 [57] later_1.1.0.1                 munsell_0.5.0                 BiocVersion_3.11.1            tools_4.0.2                  
 [61] generics_0.0.2                RSQLite_2.2.0                 fastmap_1.0.1                 stringr_1.4.0                
 [65] yaml_2.2.1                    knitr_1.29                    bit64_0.9-7                   purrr_0.3.4                  
 [69] AnnotationFilter_1.12.0       mime_0.9                      R.oo_1.23.0                   compiler_4.0.2               
 [73] rstudioapi_0.11               curl_4.3                      png_0.1-7                     interactiveDisplayBase_1.26.3
 [77] tibble_3.0.2                  stringi_1.4.6                 lattice_0.20-41               ProtGenerics_1.20.0          
 [81] Matrix_1.2-18                 permute_0.9-5                 vctrs_0.3.1                   pillar_1.4.6                 
 [85] lifecycle_0.2.0               BiocManager_1.30.10           GlobalOptions_0.1.2           bitops_1.0-6                 
 [89] httpuv_1.5.4                  R6_2.4.1                      latticeExtra_0.6-29           promises_1.1.1               
 [93] gridExtra_2.3                 dichromat_2.0-0               assertthat_0.2.1              rhdf5_2.32.2                 
 [97] openssl_1.4.2                 GenomicAlignments_1.24.0      Rsamtools_2.4.0               GenomeInfoDbData_1.2.3       
[101] hms_0.5.3                     rpart_4.1-15                  DelayedMatrixStats_1.10.1     biovizBase_1.36.0            
[105] shiny_1.5.0                   base64enc_0.1-3
TxDb GenomicFeatures • 537 views
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1
Entering edit mode

Can you try this from a clean session start? I cannot confirm. It seems your genes() method is being clobbered by some other package. Disambiguating with GenomicFeatures::genes might work better.

[Previously saved workspace restored]

> library(GenomicFeatures)
10/55 packages newly attached/loaded, see sessionInfo() for details.
> txdbmm <- makeTxDbFromGFF("Macaca_mulatta.Mmul_8.0.1.97.chr.gtf.gz")
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
> seqlevelsStyle(txdbmm) <- "UCSC"
> genes(txdbmm)
GRanges object with 30807 ranges and 1 metadata column:
                     seqnames              ranges strand |            gene_id
                        <Rle>           <IRanges>  <Rle> |        <character>
  ENSMMUG00000000001    chr20     2454421-2488376      + | ENSMMUG00000000001
  ENSMMUG00000000002    chr20     2488547-2493824      + | ENSMMUG00000000002
  ENSMMUG00000000005    chr10   84164852-84175055      - | ENSMMUG00000000005
  ENSMMUG00000000006    chr13   92226913-92233643      - | ENSMMUG00000000006
  ENSMMUG00000000007     chr3 119362812-119376267      - | ENSMMUG00000000007
                 ...      ...                 ...    ... .                ...
  ENSMMUG00000049259    chr13   90967186-90967812      - | ENSMMUG00000049259
  ENSMMUG00000049260     chr5 161054566-161057347      - | ENSMMUG00000049260
  ENSMMUG00000049261     chr3   43415682-43451824      + | ENSMMUG00000049261
  ENSMMUG00000049262    chr10   25768534-25771024      - | ENSMMUG00000049262
  ENSMMUG00000049263    chr16   47201015-47206607      - | ENSMMUG00000049263
  -------
  seqinfo: 23 sequences (1 circular) from an unspecified genome; no seqlengths
> sessionInfo()
R version 4.0.2 Patched (2020-07-06 r78792)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /udd/stvjc/VM/R-40-rex3-dist/lib64/R/lib/libRblas.so
LAPACK: /udd/stvjc/VM/R-40-rex3-dist/lib64/R/lib/libRlapack.so

locale:
[1] C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicFeatures_1.40.1 AnnotationDbi_1.50.1   Biobase_2.48.0        
[4] GenomicRanges_1.40.0   GenomeInfoDb_1.24.2    IRanges_2.22.2        
[7] S4Vectors_0.26.1       BiocGenerics_0.34.0   

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.18.2 progress_1.2.2             
 [3] tidyselect_1.1.0            purrr_0.3.4                
 [5] lattice_0.20-41             vctrs_0.3.1                
 [7] generics_0.0.2              BiocFileCache_1.12.0       
 [9] rtracklayer_1.48.0          blob_1.2.1                 
[11] XML_3.99-0.4                rlang_0.4.7                
[13] pillar_1.4.6                glue_1.4.1                 
[15] DBI_1.1.0                   BiocParallel_1.22.0        
[17] rappdirs_0.3.1              bit64_0.9-7                
[19] dbplyr_1.4.4                matrixStats_0.56.0         
[21] GenomeInfoDbData_1.2.3      lifecycle_0.2.0            
[23] stringr_1.4.0               zlibbioc_1.34.0            
[25] Biostrings_2.56.0           memoise_1.1.0              
[27] biomaRt_2.44.1              curl_4.3                   
[29] Rcpp_1.0.5                  openssl_1.4.2              
[31] DelayedArray_0.14.0         XVector_0.28.0             
[33] bit_1.1-15.2                Rsamtools_2.4.0            
[35] hms_0.5.3                   askpass_1.1                
[37] digest_0.6.25               stringi_1.4.6              
[39] dplyr_1.0.0                 grid_4.0.2                 
[41] tools_4.0.2                 bitops_1.0-6               
[43] magrittr_1.5                RCurl_1.98-1.2             
[45] RSQLite_2.2.0               tibble_3.0.3               
[47] crayon_1.3.4                pkgconfig_2.0.3            
[49] Matrix_1.2-18               ellipsis_0.3.1             
[51] prettyunits_1.1.1           assertthat_0.2.1           
[53] httr_1.4.1                  R6_2.4.1                   
[55] GenomicAlignments_1.24.0    compiler_4.0.2             
> 
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0
Entering edit mode

Hi Vincent, Sorry!! I totally missed your reply! You are, of course, absolutely right about genes() getting clobbered. I did as you suggested and everything is working out! Thanks for your help!

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2
Entering edit mode
@martin-morgan-1513
Last seen 5 days ago
United States

Good news! The heavy lifting has been done for you -- check out the EnsDb resources on AnnotationHub and the work done in the ensembldb package

library(AnnotationHub)
library(ensembldb)
hub = AnnotationHub()

and then

> query(hub, c("EnsDb", "Macaca", "97"))
AnnotationHub with 3 records
# snapshotDate(): 2020-06-18
# $dataprovider: Ensembl
# $species: Macaca nemestrina, Macaca mulatta, Macaca fascicularis
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH73898"]]'

            title
  AH73898 | Ensembl 97 EnsDb for Macaca fascicularis
  AH73903 | Ensembl 97 EnsDb for Macaca mulatta
  AH73906 | Ensembl 97 EnsDb for Macaca nemestrina
> edb = hub[["AH73903"]]
downloading 1 resources
  |======================================================================| 100%

loading from cache
>

and then

> genes(edb)
GRanges object with 32386 ranges and 8 metadata columns:
                     seqnames            ranges strand |            gene_id
                        <Rle>         <IRanges>  <Rle> |        <character>
  ENSMMUG00000005947        1       25432-42232      + | ENSMMUG00000005947
...
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0
Entering edit mode

Hi Martin,

Thanks for your reply! I did as you suggested and got the edb object:

> edb
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.4
|Creation time: Sat Jul  6 13:44:20 2019
|ensembl_version: 97
|ensembl_host: localhost
|Organism: Macaca mulatta
|taxonomy_id: 9544
|genome_build: Mmul_8.0.1
|DBSCHEMAVERSION: 2.1
| No. of genes: 32386.
| No. of transcripts: 56748.
|Protein data available.

However, some functions seem to be off (not sure if fault is on my end!):

> seqnames(edb)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'seqnames' for signature '"EnsDb"'

> keepSeqlevels(edb,"2") 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'seqinfo<-' for signature '"EnsDb"'

> cds(edb)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'cds' for signature '"EnsDb"'

genes(edb) and transcripts(edb) work, albeit with a few warnings.

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0
Entering edit mode

I think that these methods have not been implemented on the 'EnsDb' object itself, but they (other than cds()) are still available on the returned objects, e.g., seqnames(genes(edb)); perhaps other experts on the ensembldb package will respond.

Also I guess you want to do more than in your original question, so maybe a little more detail about overall objective would be helpful...

Returning to your original question and the error

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'genes' for signature '"TxDb"'

The most likely problem is that another package has defined a genes() generic, masking the generic used by GenomicFeatures (and other Bioconductor packages). So GenomicFeatures::genes(txdbm) might get you what you want.

The other possibility (less likely here) is that you have incompatible versions of Bioconductor packages; make sure BiocManager::valid() returns TRUE.

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0
Entering edit mode

Hi Martin,

Thanks for your prompt reply! I have now updated all the packages.

I wanted to create some circos plots and needed the transcript and exon level data for any individual gene. For example, something like:

gene   start     end        transcript exon
TP73 3644042 3644334 ENST00000604566.1    1
TP73 3644693 3644781 ENST00000604566.1    2
TP73 3645891 3646012 ENST00000604566.1    3
TP73 3647491 3647629 ENST00000604566.1    4
TP73 3648027 3648120 ENST00000604566.1    5
TP73 3649311 3649931 ENST00000604566.1    6

I think I am almost there with:

mydata <- exonsBy(edb, by="gene",columns = c('gene_name','gene_id','entrezid','tx_id','exon_idx'))

Thanks for your help! I have it now!

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