Not an answer, but shouldn't the API expect a Seqinfo object instead of an
arbitrary data.frame for chrominfo? Is this legacy?

Michael


On Mon, Jun 16, 2014 at 2:30 AM, Geoffrey Thomson [guest] <
guest@bioconductor.org> wrote:

> I am trying to use derfinder but it requires I have my genome features in
> the TranscriptDB from the GenomicFeatures R package.
>
> Normally one can use the inbuilt function to make a TranscriptDB from UNSC
> database however my organism, a plant, is not included in the UNSC database.
>
> Consequently I am trying to use the makeTranscriptDbFromGFF() function to
> make the TranscriptDB using a gtf file I created using tophat and cuffmerge
> on some RNA-Seq samples. However following the examples I can't get it to
> work.
>
> Here is what I've got:
>
> chrominfo <- data.frame(chrom = c("chr1", "chr2", "chr3", "chr4", "chr5",
> "chr6", "chr7", "chr8"),
>                         length= c(52991155, 45729672, 55515152, 56582383,
> 43630510, 35275713, 49172423,45569985),
>                         is_circular= rep(FALSE, 8))
>
> exons <- makeTranscriptDbFromGFF(file = "~/merged.gtf",
>                              format = "gtf",
>                              exonRankAttributeName="exon_number",
>                              chrominfo=chrominfo)
>
> Unfortunately this is the output:
>
> extracting transcript information
> Estimating transcript ranges.
> Extracting gene IDs
> Processing splicing information for gtf file.
> Prepare the 'metadata' data frame ... metadata: OK
> Error in .normargTranscripts(transcripts) :
>   values in 'transcripts$tx_strand' must be "+" or "-"
> In addition: Warning message:
> In if is.na(chrominfo)) { :
>   the condition has length > 1 and only the first element will be used
>
> What am I missing?? I also posted this question on biostar.
>
> This is the top of my gtf file:
>
> chr1    Cufflinks    exon    6524    6620    .    +    .    gene_id
> "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name
> "Medtr1g004940"; oId "Medtr1g004940.1"; nearest_ref "Medtr1g004940.1";
> class_code "="; tss_id "TSS1"; p_id "P1";
> chr1    Cufflinks    exon    7098    7366    .    +    .    gene_id
> "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name
> "Medtr1g004940"; oId "Medtr1g004940.1"; nearest_ref "Medtr1g004940.1";
> class_code "="; tss_id "TSS1"; p_id "P1";
> chr1    Cufflinks    exon    14514    14556    .    +    .    gene_id
> "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name
> "Medtr1g004950"; oId "Medtr1g004950.1"; nearest_ref "Medtr1g004950.1";
> class_code "="; tss_id "TSS2"; p_id "P2";
> chr1    Cufflinks    exon    15503    15729    .    +    .    gene_id
> "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name
> "Medtr1g004950"; oId "Medtr1g004950.1"; nearest_ref "Medtr1g004950.1";
> class_code "="; tss_id "TSS2"; p_id "P2";
> chr1    Cufflinks    exon    16283    16326    .    +    .    gene_id
> "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name
> "Medtr1g004960"; oId "Medtr1g004960.1"; nearest_ref "Medtr1g004960.1";
> class_code "="; tss_id "TSS3"; p_id "P3";
> chr1    Cufflinks    exon    17061    17304    .    +    .    gene_id
> "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name
> "Medtr1g004960"; oId "Medtr1g004960.1"; nearest_ref "Medtr1g004960.1";
> class_code "="; tss_id "TSS3"; p_id "P3";
> chr1    Cufflinks    exon    18242    18382    .    +    .    gene_id
> "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name
> "Medtr1g004960"; oId "Medtr1g004960.1"; nearest_ref "Medtr1g004960.1";
> class_code "="; tss_id "TSS3"; p_id "P3";
>
>
>
>  -- output of sessionInfo():
>
> R version 3.1.0 (2014-04-10)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C
> LC_TIME=en_NZ.UTF-8
>  [4] LC_COLLATE=en_NZ.UTF-8     LC_MONETARY=en_NZ.UTF-8
>  LC_MESSAGES=en_NZ.UTF-8
>  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_NZ.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
>  [1] splines   grid      parallel  stats     graphics  grDevices utils
> datasets
>  [9] methods   base
>
> other attached packages:
>  [1] rtracklayer_1.22.7     GenomicFeatures_1.14.5 AnnotationDbi_1.24.0
>  [4] Biobase_2.22.0         GenomicRanges_1.14.4   XVector_0.2.0
>  [7] derfinder_1.0.2        locfdr_1.1-7           HiddenMarkov_1.7-0
> [10] limma_3.18.13          Genominator_1.16.0     GenomeGraphs_1.22.0
> [13] biomaRt_2.18.0         IRanges_1.20.7         BiocGenerics_0.8.0
> [16] RSQLite_0.11.4         DBI_0.2-7
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.30.1 bitops_1.0-6      BSgenome_1.30.0   RCurl_1.95-4.1
>  Rsamtools_1.14.3
> [6] stats4_3.1.0      tools_3.1.0       XML_3.98-1.1      zlibbioc_1.8.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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