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.ocarri...@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.ocarri...@cruk.cam.ac.uk<mailto:brent.ocarri...@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 >> >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=8oRPJU9ECEg6BaCD4HZ0z_JqJraopB-KXq4CQp-k_XU&s=iRgUUzkKXXUvf7yQhdO9ZqsP_b8IeySGznd9DXQTwjU&e= >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. 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