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
Thank you! So the RangedData class has been deprecated?
Thank you! So the RangedData class has been deprecated?
Not formally but it's use is discouraged. See
?RangedData
in the IRanges package.Cheers,
H.