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bernatgel / karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
https://bernatgel.github.io/karyoploter_tutorial/
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New version and SNP-array data not working anymore #72

Closed carlacanedoribeiro closed 4 years ago

carlacanedoribeiro commented 4 years ago

Hello,

Yesterday, I updated the package and I try to produce a graph with SNP-array data as usual, and there was an error. It happens in this step:

**snp.data <- toGRanges(ind1[c("Chr", "Position", "Position", "B.Allele.Freq", "Log.R.Ratio")])**
names(mcols(snp.data)) <- c("BAF", "LRR")
seqlevelsStyle(snp.data) <- "UCSC"

The information R gives is "Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 57: at least two out of 'start', 'end', and 'width', must be supplied." Could you help to resolve this issue, please?

This is the file: _1.txt

bernatgel commented 4 years ago

HI, could you send me the output of sessionInfo() so I can see the exact version you are using?

Thanks

On Sat, Apr 18, 2020 at 5:51 PM cfc21 notifications@github.com wrote:

Hello,

Yesterday, I updated the package and I try to produce a graph with SNP-array data as usual, and there was an error. It happens in this step:

snp.data <- toGRanges(ind1[c("Chr", "Position", "Position", "B.Allele.Freq", "Log.R.Ratio")]) names(mcols(snp.data)) <- c("BAF", "LRR") seqlevelsStyle(snp.data) <- "UCSC"

The information R gives is "Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : In range 57: at least two out of 'start', 'end', and 'width', must be supplied." Could you help to resolve this issue, please?

This is the file: _1.txt https://github.com/bernatgel/karyoploteR/files/4496920/_1.txt

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carlacanedoribeiro commented 4 years ago

Hi, thank you for the brief answer. This is the output:

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

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

other attached packages:
 [1] BSgenome_1.54.0      rtracklayer_1.46.0   Biostrings_2.54.0    XVector_0.26.0      
 [5] karyoploteR_1.12.4   regioneR_1.18.1      GenomicRanges_1.38.0 GenomeInfoDb_1.22.1 
 [9] IRanges_2.20.2       S4Vectors_0.24.4     BiocGenerics_0.32.0  dplyr_0.8.5         
[13] readr_1.3.1         

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.18.0         bitops_1.0-6                matrixStats_0.56.0         
 [4] bit64_0.9-7                 RColorBrewer_1.1-2          progress_1.2.2             
 [7] httr_1.4.1                  backports_1.1.6             tools_3.6.3                
[10] R6_2.4.1                    rpart_4.1-15                lazyeval_0.2.2             
[13] Hmisc_4.4-0                 DBI_1.1.0                   colorspace_1.4-1           
[16] nnet_7.3-12                 gridExtra_2.3               tidyselect_1.0.0           
[19] prettyunits_1.1.1           bit_1.1-15.2                curl_4.3                   
[22] compiler_3.6.3              cli_2.0.2                   Biobase_2.46.0             
[25] htmlTable_1.13.3            bezier_1.1.2                DelayedArray_0.12.3        
[28] checkmate_2.0.0             scales_1.1.0                askpass_1.1                
[31] rappdirs_0.3.1              stringr_1.4.0               digest_0.6.25              
[34] Rsamtools_2.2.3             foreign_0.8-75              dichromat_2.0-0            
[37] htmltools_0.4.0             base64enc_0.1-3             jpeg_0.1-8.1               
[40] pkgconfig_2.0.3             ensembldb_2.10.2            dbplyr_1.4.2               
[43] htmlwidgets_1.5.1           rlang_0.4.5                 rstudioapi_0.11            
[46] RSQLite_2.2.0               BiocParallel_1.20.1         acepack_1.4.1              
[49] VariantAnnotation_1.32.0    RCurl_1.98-1.1              magrittr_1.5               
[52] GenomeInfoDbData_1.2.2      Formula_1.2-3               Matrix_1.2-18              
[55] Rcpp_1.0.4.6                munsell_0.5.0               fansi_0.4.1                
[58] bamsignals_1.18.0           lifecycle_0.2.0             stringi_1.4.6              
[61] SummarizedExperiment_1.16.1 zlibbioc_1.32.0             BiocFileCache_1.10.2       
[64] grid_3.6.3                  blob_1.2.1                  crayon_1.3.4               
[67] lattice_0.20-38             splines_3.6.3               GenomicFeatures_1.38.2     
[70] hms_0.5.3                   knitr_1.28                  pillar_1.4.3               
[73] biomaRt_2.42.1              XML_3.99-0.3                glue_1.4.0                 
[76] biovizBase_1.34.1           latticeExtra_0.6-29         BiocManager_1.30.10        
[79] data.table_1.12.8           vctrs_0.2.4                 png_0.1-7                  
[82] gtable_0.3.0                openssl_1.4.1               purrr_0.3.3                
[85] assertthat_0.2.1            ggplot2_3.3.0               xfun_0.13                  
[88] AnnotationFilter_1.10.0     survival_3.1-8              tibble_3.0.0               
[91] GenomicAlignments_1.22.1    AnnotationDbi_1.48.0        memoise_1.1.0              
[94] cluster_2.1.0               ellipsis_0.3.0

Thank you!