Question: I can't import my gff file by `importTransprits()`,when I worked with SGSeq.
gravatar for 2315440517
7 months ago by
23154405170 wrote:

I have some trouble when I worked with SGSeq. The species that we study has no available transcription annotation from TxDb, so I need to import my own gff file by function importTranscripts(), but I can't achieve it with the error "Error: subscript contains invalid names". I wander either the fault of my oprions or the something wrong with my gff file.

These are my code:

## "D:\\bioinformation\\Triplophysarosa\\05.Annotation\\02.Gene_Prediction\\Triplophysarosa.evm.gff"
##[1] TRUE
importTranscripts("D:\\bioinformation\\Triplophysarosa\\05.Annotation\\02.Gene_Prediction\\Triplophysarosa.evm.gff",tag_tx = "contig1",tag_gene = "evm.TU.contig365.6")
 Hide Traceback
Error: subscript contains invalid names
stop(wmsg(...), call. = FALSE)
.subscript_error("subscript contains invalid ", what)
NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
NSBS(i, x, exact = exact, strict.upper.bound = !allow.append, allow.NAs = allow.NAs)
normalizeSingleBracketSubscript(j, xstub)
mcols(exons)[c(tag_tx, tag_gene)]
mcols(exons)[c(tag_tx, tag_gene)]
data.frame(mcols(exons)[c(tag_tx, tag_gene)])
unique(data.frame(mcols(exons)[c(tag_tx, tag_gene)]))
importTranscripts(fname, tag_tx = "contig1", tag_gene = "evm.TU.contig365.6")
R version 3.5.2 (2018-12-20)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 x64 (build 7600)

Matrix products: default

[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936   
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C                                                   
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices
[6] utils     datasets  methods   base     

other attached packages:
 [1] SGSeq_1.16.2               
 [2] SummarizedExperiment_1.12.0
 [3] DelayedArray_0.8.0         
 [4] BiocParallel_1.16.6        
 [5] matrixStats_0.54.0         
 [6] Biobase_2.42.0             
 [7] Rsamtools_1.34.1           
 [8] Biostrings_2.50.2          
 [9] XVector_0.22.0             
[10] GenomicRanges_1.34.0       
[11] GenomeInfoDb_1.18.2        
[12] IRanges_2.16.0             
[13] S4Vectors_0.20.1           
[14] BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
 [1] magrittr_1.5             GenomicFeatures_1.34.4  
 [3] gtable_0.2.0             zlibbioc_1.28.0         
 [5] memoise_1.1.0            hms_0.4.2               
 [7] RCurl_1.95-4.12          pillar_1.3.1            
 [9] progress_1.2.0           stringr_1.4.0           
[11] lattice_0.20-38          rtracklayer_1.42.2      
[13] bit_1.1-14               plyr_1.8.4              
[15] knitr_1.22               GenomicAlignments_1.18.1
[17] igraph_1.2.4             pkgconfig_2.0.2         
[19] Matrix_1.2-15            R6_2.4.0                
[21] GenomeInfoDbData_1.2.0   digest_0.6.18           
[23] xfun_0.5                 colorspace_1.4-0        
[25] AnnotationDbi_1.44.0     stringi_1.3.1           
[27] lazyeval_0.2.1           yaml_2.2.0              
[29] RSQLite_2.1.1            tibble_2.0.1            
[31] httr_1.4.0               compiler_3.5.2          
[33] bit64_0.9-7              munsell_0.5.0           
[35] DBI_1.0.0                Rcpp_1.0.0              
[37] biomaRt_2.38.0           XML_3.98-1.19           
[39] RUnit_0.4.32             assertthat_0.2.0        
[41] blob_1.1.1               ggplot2_3.1.0           
[43] prettyunits_1.0.2        tools_3.5.2             
[45] bitops_1.0-6             scales_1.0.0            
[47] crayon_1.3.4             rlang_0.3.1             
[49] grid_3.5.2  
annotation software error • 168 views
ADD COMMENTlink modified 7 months ago by Leonard Goldstein80 • written 7 months ago by 23154405170
Answer: I can't import my gff file by `importTransprits()`,when I worked with SGSeq.
gravatar for Leonard Goldstein
7 months ago by
United States
Leonard Goldstein80 wrote:

When posting a question about a software package, please always tag your post with the package name. This triggers an automatic email from the system to the package maintainer.

Regarding your question -- the tag_tx and tag_gene arguments are for specifying names of the relevant GFF tags. Please try

importTranscripts("D:\\bioinformation\\Triplophysarosa\\05.Annotation\\02.Gene_Prediction\\Triplophysarosa.evm.gff",tag_tx = "ID",tag_gene = "Name")
ADD COMMENTlink written 7 months ago by Leonard Goldstein80

Thank you very much, Imy problem has been solved.

ADD REPLYlink written 7 months ago by 23154405170

Dear professor, I have another question,whether I can use SGSeq package to recognize all of splice events accross the whole genome, only run it once. Or I just can get the splice events from a particular gene for once running?

ADD REPLYlink written 7 months ago by 23154405170

Both are possible. Please see vignette section 6 for an example on how to analyze a particular region of the genome using the which argument. If no region is specified the analysis is genome-wide. Depending on your data set, genome-wide predictions can be computationally intensive. In case you run into problems, please see vignette section 13 for considerations about parallelization and memory requirements.

ADD REPLYlink written 6 months ago by Leonard Goldstein80
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