I am receiving the following "unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’ " error when using the annotation function. tss <- annotate_features(tss, genome_annotation = annotation, upstream = 200, downstream = 50) . I looked through the fixes described with relation to ChIPseeker but none seem to fit this situation. The seqnames in the tss/tsr of the TSRexploreR object appear to match the GFF. The seqnames for the TSRexploreR object are shown below as well as lines from the gff to show the naming conventions are the same. I also show the genome_annotation section of the TSRexploreR object. If someone could point me in the right direction or tell me how to access the content of the TxDb object so I can try to troubleshoot, it would be greatly appreciated.
$genome_annotation
TxDb object:
Db type: TxDb
Supporting package: GenomicFeatures
Data source: chr1.gff
Organism: NA
Taxonomy ID: NA
miRBase build ID: NA
Genome: NA
Nb of transcripts: 2331
Db created by: GenomicFeatures package from Bioconductor
Creation time: 2023-03-27 12:06:08 -0700 (Mon, 27 Mar 2023)
GenomicFeatures version at creation time: 1.46.1
RSQLite version at creation time: 2.3.0
DBSCHEMAVERSION: 1.2
I am receiving the following "unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’ " error when using the annotation function. tss <- annotate_features(tss, genome_annotation = annotation, upstream = 200, downstream = 50) . I looked through the fixes described with relation to ChIPseeker but none seem to fit this situation. The seqnames in the tss/tsr of the TSRexploreR object appear to match the GFF. The seqnames for the TSRexploreR object are shown below as well as lines from the gff to show the naming conventions are the same. I also show the genome_annotation section of the TSRexploreR object. If someone could point me in the right direction or tell me how to access the content of the TxDb object so I can try to troubleshoot, it would be greatly appreciated.
$genome_annotation TxDb object: Db type: TxDb Supporting package: GenomicFeatures Data source: chr1.gff Organism: NA Taxonomy ID: NA miRBase build ID: NA Genome: NA Nb of transcripts: 2331 Db created by: GenomicFeatures package from Bioconductor Creation time: 2023-03-27 12:06:08 -0700 (Mon, 27 Mar 2023) GenomicFeatures version at creation time: 1.46.1 RSQLite version at creation time: 2.3.0 DBSCHEMAVERSION: 1.2
$TSRs$raw$HJ2 seqnames start end width strand score n_unique normalized_score FHASH 1: chr1 15881 15920 40 + 26 4 8 chr1:15881:15920:+ 2: chr1 27592 27592 1 + 10 2 4 chr1:27592:27592:+ 3: chr1 45606 45606 1 + 14 2 4 chr1:45606:45606:+ 4: chr1 178016 178019 4 + 130 8 16 chr1:178016:178019:+ 5: chr1 192307 192307 1 + 52 2 4 chr1:192307:192307:+chr1 funannotate mRNA 4782 7654 . + . ID=PI_01chrm0001-T1;Parent=PI_01chrm0001;product=hypotheticalprotein; chr1 funannotate mRNA 7961 8721 . + . ID=PI_01chrm0002-T1;Parent=PI_01chrm0002;product=hypotheticalprotein; chr1 funannotate mRNA 9008 9388 . - . ID=PI_01chrm0003-T1;Parent=PI_01chrm0003;product=hypotheticalprotein; chr1 funannotate mRNA 10517 12893 . - . ID=PI_01chrm0004-T1;Parent=PI_01chrm0004;product=hypotheticalprotein; chr1 funannotate mRNA 14766 15506 . + . ID=PI_01chrm0005-T1;Parent=PI_01chrm0005;product=hypotheticalprotein;