[Bioc-devel] RangedData objects deprecated
Pages, Herve
hp@ge@ @end|ng |rom |redhutch@org
Thu Dec 5 21:01:02 CET 2019
On 12/4/19 17:39, Vincent Carey wrote:
> The RangedData objects are still viable with the software you are using,
> but trying
> to set colnames will trigger an error. In Bioc 3.11 you won't even be able
> to use
> the RangedData class at all. So an intervention is needed now.
>
> The RangedData objects that were serialized or created in your workflow
> should
> be converted to GRanges or GRangesList as appropriate, using as(...,
> "GRanges")
>
> Code that attempts to set the column names can be changed to use
> colnames(mcols(...))
>
> The ichorCNA package man pages don't include examples and I see no example
> data with the package.
>
> You might get a sense of what needs to be done in the following.
>
> library(GenomicRanges)
>
> ranges <- IRanges(c(1,2,3),c(4,5,6))
>
> filter <- c(1L, 0L, 1L)
>
> score <- c(10L, 2L, NA)
>
>
> ## constructing RangedData instances
>
> ## no variables
>
> rd <- RangedData(ranges, filter, vals = score) # will not work at all
>
> # in Bioc 3.11
>
> gr = as(rd, "GRanges")
>
> colnames(mcols(gr))
Exactly. Note that turning your serialized RangedData objects into
GRanges or GRangesList objects should be a one-time operation, not
something that your make.ichor.summary.R script should do on-the-fly
each time a serialized RangedData object is loaded.
More precisely, you need to proceed in 2 steps:
1. Apply the 'rd <- readRDS(); gr <- as(rd, "GRanges"); saveRDS(gr, )'
sequence on each serialized RangedData instance.
2. Adapt your make.ichor.summary.R script to make it work on GRanges
objects instead of RangedData objects (minor changes usually needed e.g.
'colnames(mcols(gr)) <- value' instead of 'colnames(rd) <- value' as
Vince suggested)
Hope this helps,
H.
>
>
> On Wed, Dec 4, 2019 at 7:34 PM Brent O'Carrigan <
> Brent.OCarrigan using cruk.cam.ac.uk> wrote:
>
>> Dear Bioc devel team,
>>
>> Can you advise how to amend the following code to update references to
>> RangedData objects?
>>
>> I’m running the Broad ichorCNA, which had a similar issue described in the
>> package internal code, which I gather has been addressed
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_broadinstitute_ichorCNA_issues_50&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8oRPJU9ECEg6BaCD4HZ0z_JqJraopB-KXq4CQp-k_XU&s=7r8ACX79DIcnADc07RT-mLiEoY68jMpiN9xYCJoLC0o&e=
>>
>> A colleague has written a wrapper script in part of our shared pipeline,
>> which I think was under R 3.5.3, and I think the RangedData references in
>> this script may need updating - which I have not been able to do.
>>
>> Kind regards,
>>
>> Dr Brent O'Carrigan
>> Clinical Research Training Fellow | PhD candidate
>> CRUK Cambridge Institute | Caldas Group
>> Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE
>> E: Brent.OCarrigan using cruk.cam.ac.uk<mailto:Brent.OCarrigan using cruk.cam.ac.uk>
>> | T: (+44) 01223 769500
>>
>>> source('make.ichor.summary.R')
>> data.table 1.12.6 using 10 threads (see ?getDTthreads). Latest news:
>> r-datatable.com
>> Loading required package: HMMcopy
>> Loading required package: IRanges
>> Loading required package: BiocGenerics
>> Loading required package: parallel
>>
>> Attaching package: ‘BiocGenerics’
>>
>> The following objects are masked from ‘package:parallel’:
>>
>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>> clusterExport, clusterMap, parApply, parCapply, parLapply,
>> parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following objects are masked from ‘package:stats’:
>>
>> IQR, mad, sd, var, xtabs
>>
>> The following objects are masked from ‘package:base’:
>>
>> anyDuplicated, append, as.data.frame, basename, cbind, colnames,
>> dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
>> grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
>> order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
>> rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
>> union, unique, unsplit, which, which.max, which.min
>>
>> Loading required package: S4Vectors
>> Loading required package: stats4
>>
>> Attaching package: ‘S4Vectors’
>>
>> The following objects are masked from ‘package:data.table’:
>>
>> first, second
>>
>> The following object is masked from ‘package:base’:
>>
>> expand.grid
>>
>>
>> Attaching package: ‘IRanges’
>>
>> The following object is masked from ‘package:data.table’:
>>
>> shift
>>
>> Loading required package: geneplotter
>> Loading required package: Biobase
>> Welcome to Bioconductor
>>
>> Vignettes contain introductory material; view with
>> 'browseVignettes()'. To cite Bioconductor, see
>> 'citation("Biobase")', and for packages 'citation("pkgname")'.
>>
>> Loading required package: lattice
>> Loading required package: annotate
>> Loading required package: AnnotationDbi
>> Loading required package: XML
>> Loading required package: ichorCNA
>>
>> Attaching package: ‘ichorCNA’
>>
>> The following object is masked from ‘package:HMMcopy’:
>>
>> HMMsegment
>>
>> Loading required package: GenomicRanges
>> Loading required package: GenomeInfoDb
>> [1] "./ichor/ichor.default/raw/041V10.sorted.dedupped.RDS"
>> [1] "Running ichorCNA"
>> Error: RangedData objects are deprecated and the colnames setter for
>> RangedData objects is now defunct. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> In addition: Warning messages:
>> 1: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> 2: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> 3: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> 4: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> 5: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> 6: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> 7: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>> 8: RangedData objects are deprecated. Please migrate your code to use
>> GRanges or GRangesList objects instead. See IMPORTANT NOTE in
>> ?RangedData
>>
>>
>>> sessionInfo()
>> R version 3.6.1 (2019-07-05)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: CentOS Linux 7 (Core)
>>
>> Matrix products: default
>> BLAS: /home/bioinformatics/software/R/R-3.6.1/lib64/R/lib/libRblas.so
>> LAPACK: /home/bioinformatics/software/R/R-3.6.1/lib64/R/lib/libRlapack.so
>>
>> locale:
>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4 parallel stats graphics grDevices utils datasets
>> [8] methods base
>>
>> other attached packages:
>> [1] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 ichorCNA_0.3.2
>> [4] HMMcopy_1.26.0 geneplotter_1.64.0 annotate_1.64.0
>> [7] XML_3.98-1.20 AnnotationDbi_1.48.0 lattice_0.20-38
>> [10] Biobase_2.46.0 IRanges_2.20.0 S4Vectors_0.24.0
>> [13] BiocGenerics_0.32.0 data.table_1.12.6
>>
>> loaded via a namespace (and not attached):
>> [1] Rcpp_1.0.3 pillar_1.4.2 compiler_3.6.1
>> [4] RColorBrewer_1.1-2 plyr_1.8.4 XVector_0.26.0
>> [7] zlibbioc_1.32.0 bitops_1.0-6 zeallot_0.1.0
>> [10] digest_0.6.23 bit_1.1-14 RSQLite_2.1.3
>> [13] memoise_1.1.0 tibble_2.1.3 pkgconfig_2.0.3
>> [16] rlang_0.4.2 DBI_1.0.0 GenomeInfoDbData_1.2.2
>> [19] vctrs_0.2.0 bit64_0.9-7 grid_3.6.1
>> [22] blob_1.2.0 backports_1.1.5 xtable_1.8-4
>> [25] RCurl_1.95-4.12 crayon_1.3.4
>>
>>
>>
>> _______________________________________________
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>>
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages using fredhutch.org
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Fax: (206) 667-1319
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