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Question: regarding makeTranscriptDbFromGFF
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gravatar for deepika lakhwani
4.2 years ago by
deepika lakhwani170 wrote:
Hello I apologize for bothering you again. I wanted to use makeTranscriptDbFromGFF function but after loading the Genomicfeatures package and run makeTranscriptDbFromGFF(). I got error Error: could not find function "makeTranscriptDbFromGFF" I do not know that What am I doing wrong. I ran: > txdb <-makeTranscriptDbFromGFF(file = 'mm9.gtf', format = "gtf",exonRankAttributeName = "exon_number", chrominfo = chrominfo, dataSource = "UCSC", species = "Mus musculus") Error: could not find function "makeTranscriptDbFromGFF" then i ran makeTranscriptDbFromGFF() Error: could not find function "makeTranscriptDbFromGFF" please resolve my problem. thanking you regards deepika [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.2 years ago by James W. MacDonald45k • written 4.2 years ago by deepika lakhwani170
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gravatar for James W. MacDonald
4.2 years ago by
United States
James W. MacDonald45k wrote:
Hi Deepika, On Wednesday, September 25, 2013 9:44:48 AM, deepika lakhwani wrote: > Hello > > I apologize for bothering you again. I wanted to use You aren't necessarily bothering anybody, but you certainly aren't helping either us or yourself. You should ALWAYS include the output of sessionInfo() when you send a question, because that will show us what you actually did, rather than what you said you did. It will also let us know which version of R/BioC you are using. As an example, you say you loaded the Genomicfeatures (sic) package. Since there is no such package, it is not unexpected that you would not be able to find the function you seek. I have no such problem when I load GenomicFeatures: > library(GenomicFeatures) > makeTranscriptDbFromGFF function (file, format = c("gff3", "gtf"), exonRankAttributeName = NULL, gffGeneIdAttributeName = NULL, chrominfo = NULL, dataSource = NA, species = NA, circ_seqs = DEFAULT_CIRC_SEQS, miRBaseBuild = NA) { format <- match.arg(format) feature.type <- c("gene", "mRNA", "exon", "CDS") gff <- import(file, format = format, feature.type = feature.type, asRangedData = FALSE) if (format == "gff3") { if (all(c("ID", "Parent") %in% colnames(mcols(gff)))) { tables <- .prepareGFF3Tables(gff, exonRankAttributeName, gffGeneIdAttributeName) } } else if (format == "gtf") { if (all(c("gene_id", "transcript_id") %in% colnames(mcols(gff)))) { tables <- .prepareGTFTables(gff, exonRankAttributeName) } } metadata <- .prepareGFFMetadata(file, dataSource, species, miRBaseBuild) if (is.null(chrominfo)) { message("Now generating chrominfo from available sequence names. No chromosome length information is available.") chroms <- unique(tables[["transcripts"]][["tx_chrom"]]) chrominfo <- data.frame(chrom = chroms, length = rep(NA, length(chroms)), is_circular = matchCircularity(chroms, circ_seqs)) } txdb <- makeTranscriptDb(transcripts = tables[["transcripts"]], splicings = tables[["splicings"]], genes = tables[["genes"]], chrominfo = chrominfo, metadata = metadata, reassign.ids = TRUE) txdb } <environment: namespace:genomicfeatures=""> > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6 Biobase_2.20.1 [4] GenomicRanges_1.12.5 IRanges_1.18.3 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.12.4 RSQLite_0.11.4 [9] rtracklayer_1.20.4 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 [13] zlibbioc_1.6.0 Best, Jim > makeTranscriptDbFromGFF function but after loading the Genomicfeatures > package and run makeTranscriptDbFromGFF(). I got error > > Error: could not find function "makeTranscriptDbFromGFF" > > I do not know that What am I doing wrong. > > > I ran: >> txdb <-makeTranscriptDbFromGFF(file = 'mm9.gtf', format = > "gtf",exonRankAttributeName = "exon_number", chrominfo = chrominfo, > dataSource = "UCSC", species = "Mus musculus") > Error: could not find function "makeTranscriptDbFromGFF" > > then i ran > > makeTranscriptDbFromGFF() > Error: could not find function "makeTranscriptDbFromGFF" > > > please resolve my problem. > > > > thanking you > > > regards > deepika > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.2 years ago by James W. MacDonald45k
Hello I am creating transcriptDb object from GFF file using maketranscriptDbFromGFF. I have sequencing data and mapped this data on rice genome using tophat now i want to count the overlaps of my genomic alignments with genes but when i ran it : txdb <- makeTranscriptDbFromGFF(file = "all.gff3",format="gff",dataSource=" ftp://ftp.plantbiology.msu.edu",exonRankAttributeName="exon_number",sp ecies="oryza sativa") Error in DataFrame(...) : different row counts implied by arguments and when i remove dataSource then again got the same error. txdb <- makeTranscriptDbFromGFF(file = "all.gff3", format= "gff",exonRankAttributeName= "exon_number",chrominfo = "chrominfo",species="oryza sativa") Error in DataFrame(...) : different row counts implied by arguments Finally i remove dataSource, chromoinfo but again failed. txdb <- makeTranscriptDbFromGFF(file = "all.gff3",format="gff",species="oryza sativa") extracting transcript information Extracting gene IDs extracting transcript information Processing splicing information for gff3 file. Deducing exon rank from relative coordinates provided Prepare the 'metadata' data frame ... metadata: OK Now generating chrominfo from available sequence names. No chromosome length information is available. Warning messages: 1: In .deduceExonRankings(exs, format = "gff") : Infering Exon Rankings. If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName 2: In matchCircularity(chroms, circ_seqs) : None of the strings in your circ_seqs argument match your seqnames. actually i am trying so many times but everytime i got error. please tell me how to solve this problem. sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 LC_MONETARY=English_India.1252 [4] LC_NUMERIC=C LC_TIME=English_India.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.12.4 AnnotationDbi_1.22.6 Biobase_2.20.1 GenomicRanges_1.12.5 IRanges_1.18.4 [6] BiocGenerics_0.6.0 BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-6 BSgenome_1.28.0 DBI_0.2-7 RCurl_1.95-4.1 [7] Rsamtools_1.12.4 RSQLite_0.11.4 rtracklayer_1.20.4 stats4_3.0.1 tools_3.0.1 XML_3.98-1.1 [13] zlibbioc_1.6.0 regards Deepika [[alternative HTML version deleted]]
ADD REPLYlink written 4.2 years ago by deepika lakhwani170
Hi, If your last attempt didn't work (I'll keep that portion of your email quoted below) there should be an error that was reported, but I only see warnings. Are there errors that come up after this? > Finally i remove dataSource, chromoinfo but again failed. > > txdb <- makeTranscriptDbFromGFF(file = > "all.gff3",format="gff",species="oryza sativa") > extracting transcript information > Extracting gene IDs > extracting transcript information > Processing splicing information for gff3 file. > Deducing exon rank from relative coordinates provided > Prepare the 'metadata' data frame ... metadata: OK > Now generating chrominfo from available sequence names. No chromosome > length information is available. > Warning messages: > 1: In .deduceExonRankings(exs, format = "gff") : > Infering Exon Rankings. If this is not what you expected, then please be > sure that you have provided a valid attribute for exonRankAttributeName > 2: In matchCircularity(chroms, circ_seqs) : > None of the strings in your circ_seqs argument match your seqnames. Is there something more that is outputted that's missing from your email? The fact that there are no errors reported suggests that you should now have a functional(?) `txdb` object ... do you? -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
ADD REPLYlink written 4.2 years ago by Steve Lianoglou12k
Hii... Ok, i got it. Actually i was thinking warning message also an error and yes its a fuctional txdb and trying so many fuctions and it works.If i want to add chromosome information then what should i do. I am trying but it did not work. I am learning these new things so apologize for asking very basic question. Thanks for your response. On Thu, Sep 26, 2013 at 6:59 PM, Steve Lianoglou <lianoglou.steve@gene.com>wrote: > Hi, > > If your last attempt didn't work (I'll keep that portion of your email > quoted below) there should be an error that was reported, but I only > see warnings. > > Are there errors that come up after this? > > > Finally i remove dataSource, chromoinfo but again failed. > > > > txdb <- makeTranscriptDbFromGFF(file = > > "all.gff3",format="gff",species="oryza sativa") > > extracting transcript information > > Extracting gene IDs > > extracting transcript information > > Processing splicing information for gff3 file. > > Deducing exon rank from relative coordinates provided > > Prepare the 'metadata' data frame ... metadata: OK > > Now generating chrominfo from available sequence names. No chromosome > > length information is available. > > Warning messages: > > 1: In .deduceExonRankings(exs, format = "gff") : > > Infering Exon Rankings. If this is not what you expected, then please > be > > sure that you have provided a valid attribute for exonRankAttributeName > > 2: In matchCircularity(chroms, circ_seqs) : > > None of the strings in your circ_seqs argument match your seqnames. > > Is there something more that is outputted that's missing from your > email? The fact that there are no errors reported suggests that you > should now have a functional(?) `txdb` object ... do you? > > -steve > > -- > Steve Lianoglou > Computational Biologist > Bioinformatics and Computational Biology > Genentech > [[alternative HTML version deleted]]
ADD REPLYlink written 4.2 years ago by deepika lakhwani170
Hi, On Thu, Sep 26, 2013 at 9:07 PM, deepika lakhwani <lakhwanideepika at="" gmail.com=""> wrote: > Hii... > > Ok, i got it. Actually i was thinking warning message also an error and yes > its a fuctional txdb and trying so many fuctions and it works.If i want to > add chromosome information then what should i do. I am trying but it did > not work. > I am learning these new things so apologize for asking very basic question. A great deal of effort has been put into the documentation for many of the packages you will find through bioconductor, this is especially true for the "foundational" packages -- and GenomicFeatures is one such package. GenomicFeatures is based on GenomicRanges, which in turn is based on IRanges. Please read through the vignettes for these packages which are the PDFs you'll find in the pages for each package under the "Documentation" section here with a mind to really understand them (not just skim the pages): http://bioconductor.org/packages/release/bioc/html/IRanges.html http://bioconductor.org/packages/release/bioc/html/GenomicRanges.html http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.htm l It's better to understand how these things work on a more fundamental level than to repeatedly ask for help with superficial issues until what you want magically works. It might feel slower to get going, but your terminal velocity will be a lot higher than you'll hit than not gaining this understanding in the first place. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
ADD REPLYlink written 4.2 years ago by Steve Lianoglou12k
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