Question: GOseq tutorial for not supported organisms: am I doing it correctly?
gravatar for CandiceChuDVM
3.4 years ago by
CandiceChuDVM30 wrote:

Hi all, 

I am using goseq to correct for RNA-seq length bias. Since my dog genome (canFam3) is not supported in goseq database, I tried to make TXDb object and GOmap by myself. However, I am not sure if I am doing it correctly.   

If it's correct, it could potentially be a tutorial and benefit other users since the goseq documentation isn't very self-explanatory.  

I have posted a question in BioStars but I think I could potentially get some help here.   

To prevent repetitive posting, here is the link to my R script:

And here is my `sessionInfo()`:

R version 3.2.4 (2016-03-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

[1] C

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

other attached packages:
 [1] biomaRt_2.26.1             GenomicFeatures_1.22.13   
 [3] AnnotationDbi_1.32.3       devtools_1.11.1           
 [5] goseq_1.22.0               RSQLite_1.0.0             
 [7] DBI_0.4-1                  geneLenDataBase_1.6.0     
 [9] BiasedUrn_1.07             DESeq2_1.10.1             
[11] RcppArmadillo_0.6.700.6.0  Rcpp_0.12.4               
[13] SummarizedExperiment_1.0.2 Biobase_2.30.0            
[15] GenomicRanges_1.22.4       GenomeInfoDb_1.6.3        
[17] IRanges_2.4.8              S4Vectors_0.8.11          
[19] BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] genefilter_1.52.1       locfit_1.5-9.1          splines_3.2.4          
 [4] lattice_0.20-33         colorspace_1.2-6        mgcv_1.8-12            
 [7] rtracklayer_1.30.4      chron_2.3-47            survival_2.39-4        
[10] XML_3.98-1.4            withr_1.0.1             foreign_0.8-66         
[13] BiocParallel_1.4.3      RColorBrewer_1.1-2      lambda.r_1.1.7         
[16] plyr_1.8.3              zlibbioc_1.16.0         Biostrings_2.38.4      
[19] munsell_0.4.3           gtable_0.2.0            futile.logger_1.4.1    
[22] memoise_1.0.0           latticeExtra_0.6-28     geneplotter_1.48.0     
[25] acepack_1.3-3.3         xtable_1.8-2            scales_0.4.0           
[28] Hmisc_3.17-4            annotate_1.48.0         XVector_0.10.0         
[31] Rsamtools_1.22.0        gridExtra_2.2.1         digest_0.6.9           
[34] ggplot2_2.1.0           grid_3.2.4              tools_3.2.4            
[37] bitops_1.0-6            RCurl_1.95-4.8          Formula_1.2-1          
[40] cluster_2.0.4           futile.options_1.0.0    GO.db_3.2.2            
[43] Matrix_1.2-6            data.table_1.9.6        rpart_4.1-10           
[46] nlme_3.1-128            GenomicAlignments_1.6.3 nnet_7.3-12

rnaseq biomart goseq deseq2 R • 666 views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by CandiceChuDVM30
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