alexg9010
commented
1 year ago Hi @laurahspencer,
Thanks for reporting your issue. Unfortunately, I am not able to reproduce your issue on my machine ( see attached output ).
Could you please give me more information about your session, by posting the sessionInfo()? Maybe you are using an outdated version of R or methylKit which is causing the issue.
Best, Alex
library(methylKit)
load(file = "~/R-dev/methylkit-dev/issue283/meth_10x")
getSampleID(meth_10x)
#> [1] "1" "2" "3" "4" "7" "8" "10" "11" "12" "15" "17" "18" "20"
getSampleID(unite(meth_10x))
#> uniting...
#> [1] "1" "2" "3" "4" "7" "8" "10" "11" "12" "15" "17" "18" "20"
getSampleID(unite(meth_10x, destrand = TRUE))
#> destranding...
#> uniting...
#> [1] "1" "2" "3" "4" "7" "8" "10" "11" "12" "15" "17" "18" "20"
sessionInfo()
#> R version 4.2.0 (2022-04-22)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
#> [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
#> [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] methylKit_1.22.0 GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
#> [4] IRanges_2.30.0 S4Vectors_0.34.0 BiocGenerics_0.42.0
#>
#> loaded via a namespace (and not attached):
#> [1] MatrixGenerics_1.8.1 Biobase_2.56.0
#> [3] splines_4.2.0 R.utils_2.12.0
#> [5] gtools_3.9.3 assertthat_0.2.1
#> [7] highr_0.9 GenomeInfoDbData_1.2.8
#> [9] Rsamtools_2.12.0 yaml_2.3.5
#> [11] numDeriv_2016.8-1.1 pillar_1.7.0
#> [13] lattice_0.20-45 glue_1.6.2
#> [15] limma_3.52.2 bbmle_1.0.25
#> [17] digest_0.6.29 XVector_0.36.0
#> [19] qvalue_2.28.0 colorspace_2.0-3
#> [21] htmltools_0.5.2 Matrix_1.4-1
#> [23] R.oo_1.25.0 plyr_1.8.7
#> [25] XML_3.99-0.10 pkgconfig_2.0.3
#> [27] emdbook_1.3.12 zlibbioc_1.42.0
#> [29] purrr_0.3.4 mvtnorm_1.1-3
#> [31] scales_1.2.0 BiocParallel_1.30.3
#> [33] tibble_3.1.7 styler_1.8.1
#> [35] generics_0.1.3 ggplot2_3.4.0
#> [37] ellipsis_0.3.2 SummarizedExperiment_1.26.1
#> [39] withr_2.5.0 cli_3.4.1
#> [41] magrittr_2.0.3 crayon_1.5.2
#> [43] mclust_5.4.10 evaluate_0.15
#> [45] R.methodsS3_1.8.2 fs_1.5.2
#> [47] fansi_1.0.3 R.cache_0.16.0
#> [49] MASS_7.3-56 tools_4.2.0
#> [51] data.table_1.14.2 matrixStats_0.62.0
#> [53] BiocIO_1.6.0 lifecycle_1.0.3
#> [55] stringr_1.4.0 munsell_0.5.0
#> [57] reprex_2.0.2 DelayedArray_0.22.0
#> [59] Biostrings_2.64.0 compiler_4.2.0
#> [61] fastseg_1.42.0 rlang_1.0.6
#> [63] grid_4.2.0 RCurl_1.98-1.7
#> [65] rstudioapi_0.14 rjson_0.2.21
#> [67] bitops_1.0-7 rmarkdown_2.14
#> [69] restfulr_0.0.15 gtable_0.3.0
#> [71] codetools_0.2-18 DBI_1.1.3
#> [73] reshape2_1.4.4 R6_2.5.1
#> [75] GenomicAlignments_1.32.1 knitr_1.39
#> [77] dplyr_1.0.9 rtracklayer_1.56.1
#> [79] bdsmatrix_1.3-6 fastmap_1.1.0
#> [81] utf8_1.2.2 stringi_1.7.8
#> [83] parallel_4.2.0 Rcpp_1.0.9
#> [85] vctrs_0.5.1 tidyselect_1.2.0
#> [87] xfun_0.36 coda_0.19-4Created on 2023-05-16 with reprex v2.0.2
laurahspencer
When running the unite() function in methylKit, the sample IDs specified in the methylRaw object are not correctly being assigned. I have 13 samples, with the IDs 1, 2, 3, 4, 7, 8, 10, 11, 12, 15, 17, 18, 20 (i.e. not all consecutive numbers). When I run unite() the resulting columns of data in the methylBase object contain sample IDs #1-13. Thinking that unite() renamed them consecutively I tried to spot-check the data to see if I can confidently rename the columns using my original IDs, but the data doesn't line up (possibly because I've destranded, but I can't be sure). How can I make sure that the correct sample IDs are transferred over to the methylBase object?
Here is a directory containing the methylRaw object
meth_10x, and using the codemethylKit::unite(meth_10x, destrand=TRUE)I created the methylBase objectmeth_unite_10x, which has the incorrect sample IDs.