[rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
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@darya-vanichkina-6050
Last seen 7.1 years ago
Australia/Centenary Institute Universit…
 

I'm trying to import a gencode mouse GTF file into R:

GTF.exon <- import.gff("../20151202_GencodeAnnotationGTFexplore/gencode.vM8.primary_assembly.annotation.gtf", format="gtf", genome="GRCm38.p4", asRangedData=F, feature.type="exon")

and am getting an error while using some legacy code with regards to the asRangedData=FALSE argument:

Error in .local(con, format, text, ...) : 
  unused argument (asRangedData = FALSE)

I'm afraid that I can't find a clear explanation about what this argument was supposed to do*, and hence I'm not sure whether I should be coding for this type of data handling in a different manner now.

What did asRangedData do, and why has it been removed from rtracklayer?

Thanks in advance,
Darya

 

* I have found the following documentation, but am not sure what it means at the functional level, i.e. how it can/cannot affect my results:

GenomicData(ranges, ..., strand = NULL, chrom = NULL, genome = NULL, asRangedData = FALSE): 

IfasRangedData is FALSE (the default), constructs a GRanges instance with the given ranges and variables in ... (see theGRanges constructor). If asRangedData is TRUE, constructs a RangedData instance with the given ranges and variables in ....

...

So I would have been getting a GRanges instance as opposed to a RangedData - what does this mean in practical terms?

 

> sessionInfo()

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

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

other attached packages:
 [1] Rsamtools_1.22.0     Biostrings_2.38.2    XVector_0.10.0       rtracklayer_1.30.1   GenomicRanges_1.22.2 GenomeInfoDb_1.6.1   IRanges_2.4.6       
 [8] S4Vectors_0.8.5      BiocGenerics_0.16.1  reshape2_1.4.1       RColorBrewer_1.1-2   data.table_1.9.6     ggplot2_2.0.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2                knitr_1.11                 magrittr_1.5               GenomicAlignments_1.6.1    zlibbioc_1.16.0           
 [6] BiocParallel_1.4.3         munsell_0.4.2              colorspace_1.2-6           stringr_1.0.0              plyr_1.8.3                
[11] tools_3.2.2                SummarizedExperiment_1.0.1 grid_3.2.2                 Biobase_2.30.0             gtable_0.1.2              
[16] lambda.r_1.1.7             futile.logger_1.4.1        futile.options_1.0.0       bitops_1.0-6               RCurl_1.95-4.7            
[21] stringi_1.0-1              scales_0.3.0               XML_3.98-1.3               chron_2.3-47  
software error rtracklayer • 2.9k views
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@michael-lawrence-3846
Last seen 2.3 years ago
United States

The rtracklayer import methods always return a GRanges these days, so there is no consequence to removing that argument.

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Thank you! So the RangedData class has been deprecated? 

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Thank you! So the RangedData class has been deprecated? 

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Not formally but it's use is discouraged. See ?RangedData in the IRanges package.

Cheers,

H.

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