Question: Could not find function "makeTranscriptDbFromGFF"
gravatar for Gary
2.2 years ago by
Gary20 wrote:


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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> 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"
ADD COMMENTlink modified 2.2 years ago by Michael Lawrence11k • written 2.2 years ago by Gary20
Answer: Could not find function "makeTranscriptDbFromGFF"
gravatar for Michael Lawrence
2.2 years ago by
United States
Michael Lawrence11k wrote:

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.

ADD COMMENTlink written 2.2 years ago by Michael Lawrence11k

You are right and thank you so much.

ADD REPLYlink written 2.2 years ago by Gary20
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