Could not find function "makeTranscriptDbFromGFF"
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Entering edit mode
Gary ▴ 20
@gary-7967
Last seen 3.8 years ago

Hi,

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"
Copyright (C) 2017 The R Foundation for Statistical Computing
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, as.data.frame, cbind, colMeans,
    colnames, colSums, do.call, duplicated, eval, evalq,
    Filter, Find, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, Map, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, 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’:

    expand.grid

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")'.
> 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

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] 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
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Entering edit mode
@michael-lawrence-3846
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.

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0
Entering edit mode

You are right and thank you so much.

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