Error in mapToTranscripts

[weir12]

Hi: When I use function mapToTranscripts I get an error:

> mapToTranscripts(x, GR)
Error in .normargSeqlevels(seqnames) :
  supplied 'seqlevels' cannot contain NAs or empty strings ("")

However,table(is.na(seqlevels(GR))) table(seqlevels(GR)=="") Hint that it doesn't exist NA or empty strings traceback:

12: stop(errmsg)
11: .normargSeqlevels(seqnames)
10: Seqinfo(names(seqlengths), seqlengths)
9: new_GRanges("GRanges", seqnames = seqnames, ranges = ranges,
       strand = strand, mcols = mcols, seqlengths = seqlengths,
       seqinfo = seqinfo)
8: GRanges(names(transcripts)[transcriptsHits], xrange, strand(flat)[txHits],
       df, seqlengths = seqlengths)
7: .mapToTranscripts(x, transcripts, hits, ignore.strand, intronJunctions)
6: .local(x, transcripts, ...)
5: mapToTranscripts(x, grl, ignore.strand)
4: mapToTranscripts(x, grl, ignore.strand)
3: .local(x, transcripts, ...)
2: mapToTranscripts(x, GR)
1: mapToTranscripts(x, GR)

Supplementary information

> str(GR)
Formal class 'GRanges' [package "GenomicRanges"] with 7 slots
  ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. ..@ values         : Factor w/ 440 levels "NC_000001.11",..: 1 2 3 4 5 6 7 8 9 10 ...
  .. .. ..@ lengths        : int [1:435] 16474 12488 10350 7126 7287 8488 7809 6504 7222 7837 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. ..@ start          : int [1:178581] 11874 29926 30366 30438 69091 131068 182388 200442 487055 722046 ...
  .. .. ..@ width          : int [1:178581] 2536 1370 138 21 918 3769 2491 3542 3765 3777 ...
  .. .. ..@ NAMES          : chr [1:178581] "NR_046018.2" "XR_001737835.1" "NR_036051.1" "rna-MIR1302-2" ...
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ strand         :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 1 2 1 2 1 2 1 2 1 2 ...
  .. .. ..@ lengths        : int [1:715] 8550 7924 6458 6030 5145 5205 3683 3443 3703 3584 ...
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
  .. .. ..@ seqnames   : chr [1:440] "NC_000001.11" "NC_000002.12" "NC_000003.12" "NC_000004.12" ...
  .. .. ..@ seqlengths : int [1:440] NA NA NA NA NA NA NA NA NA NA ...
  .. .. ..@ is_circular: logi [1:440] NA NA NA NA NA NA ...
  .. .. ..@ genome     : chr [1:440] NA NA NA NA ...
  ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 178581
  .. .. ..@ listData       :List of 2
  .. .. .. ..$ tx_id  : int [1:178581] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. .. ..$ tx_name: chr [1:178581] "NR_046018.2" "XR_001737835.1" "NR_036051.1" "rna-MIR1302-2" ...
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ elementType    : chr "ANY"
  ..@ metadata       :List of 1
  .. ..$ genomeInfo:List of 15
  .. .. ..$ Db type                                 : chr "TxDb"
  .. .. ..$ Supporting package                      : chr "GenomicFeatures"
  .. .. ..$ Data source                             : chr "/home/weir/RNAedit/human_test/reference/GCF_000001405.38_GRCh38.p12_genomic.gff"
  .. .. ..$ Organism                                : chr NA
  .. .. ..$ Taxonomy ID                             : chr NA
  .. .. ..$ miRBase build ID                        : chr NA
  .. .. ..$ Genome                                  : chr NA
  .. .. ..$ transcript_nrow                         : chr "178581"
  .. .. ..$ exon_nrow                               : chr "1945509"
  .. .. ..$ cds_nrow                                : chr "1460272"
  .. .. ..$ Db created by                           : chr "GenomicFeatures package from Bioconductor"
  .. .. ..$ Creation time                           : chr "2019-06-17 22:46:48 +0800 (Mon, 17 Jun 2019)"
  .. .. ..$ GenomicFeatures version at creation time: chr "1.34.8"
  .. .. ..$ RSQLite version at creation time        : chr "2.1.1"
  .. .. ..$ DBSCHEMAVERSION                         : chr "1.2"

[hpages]

Hi,

Note that you're not telling us anything about x. Please provide the code that allows us to reproduce the problem. Also show us the output of your sessionInfo().

Thanks!

[hpages]

Also mapToTranscripts() does not belong to the GenomicRanges package so I'm closing this issue.

Please create a new issue under the appropriate package (GenomicFeatures) with reproducible example and sessionInfo() if you're still having problems with this.