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Question: [rtracklayer] Error in .local(con, format, text, ...) : unused argument (asRangedData = FALSE)
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gravatar for Darya Vanichkina
23 months ago by
Australia/Centenary Institute University of Sydney
Darya Vanichkina90 wrote:
 

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  
ADD COMMENTlink modified 23 months ago by Michael Lawrence9.8k • written 23 months ago by Darya Vanichkina90
2
gravatar for Michael Lawrence
23 months ago by
United States
Michael Lawrence9.8k wrote:

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

ADD COMMENTlink written 23 months ago by Michael Lawrence9.8k

Thank you! So the RangedData class has been deprecated? 

ADD REPLYlink written 23 months ago by Darya Vanichkina90

Thank you! So the RangedData class has been deprecated? 

ADD REPLYlink written 23 months ago by Darya Vanichkina90

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

Cheers,

H.

ADD REPLYlink modified 23 months ago • written 23 months ago by Hervé Pagès ♦♦ 13k
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