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ShixiangWang / sigminer

šŸŒ² An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://shixiangwang.github.io/sigminer/
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Warning when running example data through sigminer rearrangement tally #458

Closed selkamand closed 1 month ago

selkamand commented 3 months ago

Hi @ShixiangWang,

Another question sorry :)

Running "toy_sv.rds" through sig_tally as described in sigminer book throws warnings that aren't included in the book. Example warnings are described below. Is it expected that these warnings should come up with the example toy dataset or is something going wrong? 

#> Warning: pcf is not run for sample 1 on chromosome arm 22q because all
#> observations are missing. NA is returned.

Warning in .merge_two_Seqinfo_objects(x, y): Each of the 2 combined objects has sequence levels not in the other:
#>   - in 'x': 10, 12, 13, 14, 15, 16, 17, 18, 19, 2, 20, 21, 22, 4, 5, 6, 7, 8, 9
#>   - in 'y': Y
#>   Make sure to always combine/compare objects based on the same reference

Full reprex:

library(sigminer)
#> Registered S3 method overwritten by 'sigminer':
#>   method      from
#>   print.bytes Rcpp
#> sigminer version 2.3.1
#> - Star me at https://github.com/ShixiangWang/sigminer
#> - Run hello() to see usage and citation.

sv <- readRDS(system.file("extdata", "toy_sv.rds", package = "sigminer", mustWork = TRUE))
rs <- read_sv_as_rs(sv)
#> succesfully read RS!
tally_rs <- sig_tally(rs)
#> ā„¹ [2024-06-07 14:09:32.642524]: Started.
#> āœ” [2024-06-07 14:09:32.646027]: Successfully get RS list!
#> [1] "Getting clustered info..."
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xp 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21p 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xp 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xp 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 21p 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xp 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xp 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm Yq 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xp 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21p 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm Xp 
#> pcf finished for chromosome arm Xq 
#> pcf finished for chromosome arm Yp 
#> pcf finished for chromosome arm Yq 
#> [1] "Getting type of segment ..."
#> [1] "Getting distance of two rearrange segments ..."
#> Warning: pcf is not run for sample 1 on chromosome arm 22q because all
#> observations are missing. NA is returned.
#> Warning: pcf is not run for sample 1 on chromosome arm 22q because all
#> observations are missing. NA is returned.
#> Warning in .merge_two_Seqinfo_objects(x, y): Each of the 2 combined objects has sequence levels not in the other:
#>   - in 'x': 1, 10, 12, 15, 16, 17, 2, 20, 21, 3, 4, 6, 7, 8, 9
#>   - in 'y': X
#>   Make sure to always combine/compare objects based on the same reference
#>   genome (use suppressWarnings() to suppress this warning).
#> Warning: pcf is not run for sample 1 on chromosome arm 21p because all
#> observations are missing. NA is returned.
#> Warning: pcf is not run for sample 1 on chromosome arm 22q because all
#> observations are missing. NA is returned.
#> Warning: pcf is not run for sample 1 on chromosome arm 19p because all
#> observations are missing. NA is returned.
#> Warning: pcf is not run for sample 1 on chromosome arm 17q because all
#> observations are missing. NA is returned.
#> Warning: pcf is not run for sample 1 on chromosome arm 18q because all
#> observations are missing. NA is returned.
#> Warning in .merge_two_Seqinfo_objects(x, y): Each of the 2 combined objects has sequence levels not in the other:
#>   - in 'x': 10, 12, 13, 14, 15, 16, 17, 18, 19, 2, 20, 21, 22, 4, 5, 6, 7, 8, 9
#>   - in 'y': Y
#>   Make sure to always combine/compare objects based on the same reference
#>   genome (use suppressWarnings() to suppress this warning).
#> Warning: pcf is not run for sample 1 on chromosome arm Xp because all
#> observations are missing. NA is returned.
#> Warning: pcf is not run for sample 1 on chromosome arm 3q because all
#> observations are missing. NA is returned.
#> āœ” [2024-06-07 14:09:34.380307]: Successfully get RS features!
#> āœ” [2024-06-07 14:09:34.381502]: Successfully get RS component!
#> āœ” [2024-06-07 14:09:34.391012]: Successfully get RS matrix!
#> ā„¹ [2024-06-07 14:09:34.391873]: 1.749 secs elapsed.
sessionInfo()
#> R version 4.4.0 (2024-04-24)
#> Platform: aarch64-apple-darwin20
#> Running under: macOS Sonoma 14.4.1
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
#> 
#> Random number generation:
#>  RNG:     L'Ecuyer-CMRG 
#>  Normal:  Inversion 
#>  Sample:  Rejection 
#>  
#> locale:
#> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
#> 
#> time zone: Australia/Sydney
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] purrr_1.0.2         sigminer_2.3.1      Biobase_2.64.0     
#> [4] BiocGenerics_0.50.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] gtable_0.3.5            xfun_0.44               ggplot2_3.5.1          
#>  [4] vctrs_0.6.5             tools_4.4.0             generics_0.1.3         
#>  [7] stats4_4.4.0            parallel_4.4.0          tibble_3.2.1           
#> [10] fansi_1.0.6             cluster_2.1.6           pkgconfig_2.0.3        
#> [13] data.table_1.15.4       RColorBrewer_1.1-3      S4Vectors_0.42.0       
#> [16] rngtools_1.5.2          lifecycle_1.0.4         GenomeInfoDbData_1.2.12
#> [19] compiler_4.4.0          stringr_1.5.1           munsell_0.5.1          
#> [22] codetools_0.2-20        GenomeInfoDb_1.40.1     htmltools_0.5.8.1      
#> [25] yaml_2.3.8              pillar_1.9.0            furrr_0.3.1            
#> [28] iterators_1.0.14        foreach_1.5.2           parallelly_1.37.1      
#> [31] tidyselect_1.2.1        digest_0.6.35           stringi_1.8.4          
#> [34] future_1.33.2           dplyr_1.1.4             reshape2_1.4.4         
#> [37] listenv_0.9.1           fastmap_1.2.0           grid_4.4.0             
#> [40] colorspace_2.1-0        cli_3.6.2               magrittr_2.0.3         
#> [43] utf8_1.2.4              withr_3.0.0             scales_1.3.0           
#> [46] UCSC.utils_1.0.0        registry_0.5-1          XVector_0.44.0         
#> [49] rmarkdown_2.27          httr_1.4.7              globals_0.16.3         
#> [52] copynumber_1.29.0.9000  evaluate_0.23           knitr_1.47             
#> [55] GenomicRanges_1.56.0    IRanges_2.38.0          doParallel_1.0.17      
#> [58] NMF_0.27                rlang_1.1.4             Rcpp_1.0.12            
#> [61] gridBase_0.4-7          glue_1.7.0              reprex_2.1.0           
#> [64] rstudioapi_0.16.0       jsonlite_1.8.8          R6_2.5.1               
#> [67] plyr_1.8.9              zlibbioc_1.50.0         fs_1.6.4

Created on 2024-06-07 with reprex v2.1.0

ShixiangWang commented 3 months ago

The two warnings can be ignored. The first one is just not data for pcf in specific regions, use other data may not report this warning. The second one, Make sure to always combine/compare objects based on the same reference should be okay, as they are from the same reference, not like the case (one is from chr1 and the other is from 1)

selkamand commented 1 month ago

Thanks for clarifying!