Which library now contains the ssdCoverage command that used to be found in the htseqtools package for R version 4.0.1 ?
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Mick • 0
@biomickwatson
Last seen 5 months ago
United States

Given the most recent update to Bioconductor:

Ten software packages (ontoCat, spliceR, GMRP, MBttest, OperaMate, DASC, htSeqTools, PAnnBuilder, phenoDist, BrowserVizDemo) are deprecated in this release and will be removed in BioC 3.8.

How can I run the ssdCoverage command, originally found in htSeqTools, using the latest version of R and Bioconductor? Are there alternative methods that are not deprecated?

Deprecation chipseq htseqtools Bioconductor • 249 views
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Basti ▴ 150
@7d45153c
Last seen 18 hours ago
France

Hi, maybe you can run the source code of the function in your R console : https://rdrr.io/bioc/htSeqTools/src/R/ssdCoverage.R

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Thanks that was a great idea, but now I get the error:

Error in as(x, "RangedData") : 
  no method or default for coercing “GRanges” to “RangedData”

For reference here are thee details of my R session using sessionInfo():

R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/wagner-lab/sklasfeld/Projects/Blacklisting/env/r4/lib/libopenblasp-r0.3.12.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] htSeqTools_1.31.0    BSgenome_1.58.0      rtracklayer_1.50.0  
 [4] Biostrings_2.58.0    XVector_0.30.0       MASS_7.3-53.1       
 [7] Biobase_2.50.0       chromstaR_1.16.0     chromstaRData_1.16.0
[10] ggplot2_3.3.3        GenomicRanges_1.42.0 GenomeInfoDb_1.26.2 
[13] IRanges_2.24.1       S4Vectors_0.28.1     BiocGenerics_0.36.0 
[16] argparse_2.0.3      

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.20.0 reshape2_1.4.4             
 [3] lattice_0.20-41             colorspace_2.0-0           
 [5] vctrs_0.3.6                 XML_3.99-0.5               
 [7] utf8_1.1.4                  rlang_0.4.10               
 [9] pillar_1.5.1                glue_1.4.2                 
[11] withr_2.4.1                 BiocParallel_1.24.1        
[13] matrixStats_0.58.0          GenomeInfoDbData_1.2.4     
[15] foreach_1.5.1               lifecycle_1.0.0            
[17] plyr_1.8.6                  stringr_1.4.0              
[19] zlibbioc_1.36.0             MatrixGenerics_1.2.1       
[21] munsell_0.5.0               findpython_1.0.7           
[23] gtable_0.3.0                mvtnorm_1.1-1              
[25] codetools_0.2-18            bamsignals_1.22.0          
[27] doParallel_1.0.16           fansi_0.4.2                
[29] Rcpp_1.0.6                  scales_1.1.1               
[31] DelayedArray_0.16.2         jsonlite_1.7.2             
[33] Rsamtools_2.6.0             stringi_1.5.3              
[35] grid_4.0.3                  tools_4.0.3                
[37] bitops_1.0-6                magrittr_2.0.1             
[39] RCurl_1.98-1.2              tibble_3.1.0               
[41] crayon_1.4.1                pkgconfig_2.0.3            
[43] ellipsis_0.3.1              Matrix_1.3-2               
[45] iterators_1.0.13            R6_2.5.0                   
[47] GenomicAlignments_1.26.0    compiler_4.0.3
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Unfortunately it seems it is not possible to use RangedData objects anymore. You may ask for alternative functions/packages that exist and do similar things. If you really want to use this function, perhaps you can download older versions of bioconductor that can deal with it but if think it's not a good solution to downgrade version.

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