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I installed new package and added library GenomicFeatures. One of the changes in version 1.20 is renamed function makeTranscriptDbFromGFF() to makeTxDbFromGFF(), but using this new name I got an error that function cannot be found. Can you tell me why? (Btw, old function works fine)
I follow with RNA-seq workflow from http://www.bioconductor.org/help/workflows/rnaseqGene/ and using exonsBy() function I cannot extract exon_name (instead of exon names this function generates NA). Any idea why?
Can you give us the output of
packageVersion("GenomicFeatures")orsessionInfo()after you have loadedGenomicFeatures?I checked and it is ‘1.18.7’, but why if I installed it few hours ago using
source("http://bioconductor.org/biocLite.R") biocLite("GenomicFeatures")Output from sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=pl_PL.UTF-8 LC_NUMERIC=C
[3] LC_TIME=pl_PL.UTF-8 LC_COLLATE=pl_PL.UTF-8
[5] LC_MONETARY=pl_PL.UTF-8 LC_MESSAGES=pl_PL.UTF-8
[7] LC_PAPER=pl_PL.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicFeatures_1.18.7 AnnotationDbi_1.28.2 Biobase_2.26.0
[4] Rsamtools_1.18.3 Biostrings_2.34.1 XVector_0.6.0
[7] airway_1.0.0 GenomicRanges_1.18.4 GenomeInfoDb_1.2.5
[10] IRanges_2.0.1 S4Vectors_0.4.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] base64enc_0.1-3 BatchJobs_1.6 BBmisc_1.9
[4] BiocParallel_1.0.3 biomaRt_2.22.0 bitops_1.0-6
[7] brew_1.0-6 checkmate_1.6.2 codetools_0.2-14
[10] DBI_0.3.1 digest_0.6.8 fail_1.2
[13] foreach_1.4.2 GenomicAlignments_1.2.2 iterators_1.0.7
[16] magrittr_1.5 RCurl_1.95-4.7 RSQLite_1.0.0
[19] rtracklayer_1.26.3 sendmailR_1.2-1 stringi_0.5-5
[22] stringr_1.0.0 tools_3.1.2 XML_3.98-1.3
[25] zlibbioc_1.12.0
What is the output of your session info?