Could not find function "makeTranscriptDbFromGFF"
Entering edit mode
Gary ▴ 20
Last seen 3.8 years ago


I use makeTranscriptDbFromGFF in GenomicFeatures to access a mandarin duck genome annotation (.gff file) provided by our cooperators. However, it showed that Error in makeTranscriptDbFromGFF("Mandarin.gff", format = "gff") : could not find function "makeTranscriptDbFromGFF". Please see the detail below. Could you help me? Many thanks.

R version 3.4.1 (2017-06-30) -- "Single Candle"
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Platform: x86_64-apple-darwin15.6.0 (64-bit)

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> setwd("/Volumes/NCUE/20170811_Tang_MandarinDuck/20170809_ReferenceGenomeAnnotation")
> require(GenomicFeatures)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append,, cbind, colMeans,
    colnames, colSums,, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, Map, mapply, match, mget, order, paste,
    pmax,, pmin,, Position, rank, rbind,
    Reduce, rowMeans, rownames, rowSums, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:


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
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

[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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GenomicFeatures_1.28.5 AnnotationDbi_1.38.2   Biobase_2.36.2         GenomicRanges_1.28.5   GenomeInfoDb_1.12.2   
[6] IRanges_2.10.3         S4Vectors_0.14.4       BiocGenerics_0.22.0   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               XVector_0.16.0             GenomicAlignments_1.12.2   zlibbioc_1.22.0           
 [5] BiocParallel_1.10.1        bit_1.1-12                 lattice_0.20-35            rlang_0.1.2               
 [9] blob_1.1.0                 tools_3.4.1                grid_3.4.1                 SummarizedExperiment_1.6.4
[13] DBI_0.7                    matrixStats_0.52.2         bit64_0.9-7                digest_0.6.12             
[17] tibble_1.3.4               Matrix_1.2-11              GenomeInfoDbData_0.99.0    rtracklayer_1.36.4        
[21] bitops_1.0-6               RCurl_1.95-4.8             biomaRt_2.32.1             memoise_1.1.0             
[25] RSQLite_2.0                DelayedArray_0.2.7         compiler_3.4.1             Rsamtools_1.28.0          
[29] Biostrings_2.44.2          XML_3.98-1.9              
> txdb <- makeTranscriptDbFromGFF("Mandarin.gff", format="gff")
Error in makeTranscriptDbFromGFF("Mandarin.gff", format = "gff") : 
  could not find function "makeTranscriptDbFromGFF"
GenomicFeatures makeTranscriptDbFromGFF gff annotation • 3.6k views
Entering edit mode
Last seen 12 months ago
United States

I think that function has been renamed to makeTxDbFromGFF() in accordance with the change in the name of the TxDb class, through an appropriate deprecation cycle.

Entering edit mode

You are right and thank you so much.


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