getGenes can't find subjectHits

[johnstonmj]

I would like to go from transcripts back to the annotated gene names in a GTF.

I am trying this command:

geneoverlaps = getGenes("/media/michael/Storage Drive/Desktop/20161117rnaseq/reference/Mus_musculus.GRCm38.86.gtf", structure(bg_AM1)$trans, UCSC=FALSE, attribute="gene_id")

I get the following error:

Error in geneLocs[subjectHits(ol)]: could not find function "subjectHits"
Traceback:

1. getGenes("/media/michael/Storage Drive/Desktop/20161117rnaseq/reference/Mus_musculus.GRCm38.86.gtf", 
 .     structure(bg_AM1)$trans, UCSC = FALSE, attribute = "gene_id")
2. split(names(geneLocs[subjectHits(ol)]), queryHits(ol))
3. geneLocs[subjectHits(ol)]

sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.24.0 devtools_1.12.0      dplyr_0.4.3         
[4] genefilter_1.54.2    RSkittleBrewer_1.1   ballgown_2.6.0      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5                RColorBrewer_1.1-2        
 [3] GenomeInfoDb_1.8.7         XVector_0.12.1            
 [5] bitops_1.0-6               tools_3.3.1               
 [7] zlibbioc_1.18.0            digest_0.6.10             
 [9] uuid_0.1-2                 memoise_1.0.0             
[11] RSQLite_1.0.0              annotate_1.50.0           
[13] nlme_3.1-128               jsonlite_1.1              
[15] evaluate_0.10              lattice_0.20-34           
[17] mgcv_1.8-12                Matrix_1.2-7.1            
[19] DBI_0.5-1                  IRdisplay_0.4.4           
[21] IRkernel_0.7               parallel_3.3.1            
[23] withr_1.0.2                repr_0.10                 
[25] rtracklayer_1.34.1         stringr_1.1.0             
[27] Biostrings_2.40.0          S4Vectors_0.12.0          
[29] IRanges_2.8.0              stats4_3.3.1              
[31] grid_3.3.1                 Biobase_2.32.0            
[33] R6_2.2.0                   AnnotationDbi_1.36.0      
[35] survival_2.40-1            XML_3.98-1.4              
[37] BiocParallel_1.6.6         limma_3.29.0              
[39] pbdZMQ_0.2-3               sva_3.20.0                
[41] magrittr_1.5               Rsamtools_1.26.1          
[43] splines_3.3.1              BiocGenerics_0.20.0       
[45] GenomicRanges_1.26.1       GenomicAlignments_1.10.0  
[47] assertthat_0.1             SummarizedExperiment_1.4.0
[49] xtable_1.8-2               stringi_1.1.1             
[51] lazyeval_0.2.0             RCurl_1.95-4.8            
[53] crayon_1.3.2               Cairo_1.5-9               

Any ideas why it can't be found? Or how to find it?

Thanks!

[alyssafrazee]

Interesting: it looks like subjectHits was removed from the S4Vectors package in 0.12 (and renamed to to): https://github.com/Bioconductor-mirror/S4Vectors/blob/master/NEWS#L99

I'll bump the version requirement in ballgown and write a test for this kind of thing to avoid future mistakes. Unfortunately I only maintain ballgown in my spare time, so it may be a few weeks (I should have some time over the holiday break to do this). Let me know if this is super urgent and I can try to push the fix out sooner (unfortunately there's not an easy way to install an older version of a package from bioconductor :cry: -- the best workaround is to use an older version of R itself, which makes me sad).

Sorry for the bad experience here! Will post again on the issue when it's fixed.

[johnstonmj]

Thank you for the response! I know it is likely not your main focus right now.

Not super urgent, but I would like to use this feature sometime after the holidays.

Thanks for looking into it! :)

• Michael

On Mon, Dec 12, 2016 at 6:06 PM, Alyssa Frazee [email protected] wrote:

Interesting: it looks like subjectHits was removed from the S4Vectors package in 0.12 (and renamed to to): https://github.com/ Bioconductor-mirror/S4Vectors/blob/master/NEWS#L99

I'll bump the version requirement in ballgown and write a test for this kind of thing to avoid future mistakes. Unfortunately I only maintain ballgown in my spare time, so it may be a few weeks (I should have some time over the holiday break to do this). Let me know if this is super urgent and I can try to push the fix out sooner (unfortunately there's not an easy way to install an older version of a package from bioconductor 😢 -- the best workaround is to use an older version of R itself, which makes me sad).

Sorry for the bad experience here! Will post again on the issue when it's fixed.

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