unite() function reassigns sample ID's #283
Comments
|
Hi @laurahspencer, Thanks for reporting your issue. Could you please give me more information about your session, by posting the Best, 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 |
|
Interesting! Here is my session info: |
|
When I run |
|
And similarly, |
|
Ah okay, now I got what you were referring to.
These are actually the column names of the internal dataframe. They are not
generated based on the given sample ids, nor the treatment vector. They are
simply referring to the n-th sample in the object, or the n-th position of
the sample-id vector.
I hope this clears things up.
Best,
Alex
Laura H Spencer ***@***.***> schrieb am Di., 16. Mai 2023,
20:56:
… And similarly,
colnames(unite(meth_10x, destrand = TRUE))
destranding...
uniting...
[1] "chr" "start" "end" "strand" "coverage1" "numCs1" "numTs1" "coverage2" "numCs2" "numTs2" "coverage3"
[12] "numCs3" "numTs3" "coverage4" "numCs4" "numTs4" "coverage5" "numCs5" "numTs5" "coverage6" "numCs6" "numTs6"
[23] "coverage7" "numCs7" "numTs7" "coverage8" "numCs8" "numTs8" "coverage9" "numCs9" "numTs9" "coverage10" "numCs10"
[34] "numTs10" "coverage11" "numCs11" "numTs11" "coverage12" "numCs12" "numTs12" "coverage13" "numCs13" "numTs13"
—
Reply to this email directly, view it on GitHub
<#283 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ADK7JD2NVLA3AGAFMGVJ3H3XGPEUXANCNFSM6AAAAAAYCT7DYE>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
That makes sense- so when I run |
|
Yes, this should work.
Currently the only helper that we provide would be percMethylation() to
extract methylation per region per sample.
Laura H Spencer ***@***.***> schrieb am Mi., 17. Mai 2023,
23:06:
… That makes sense- so when I run getData(meth_unite_10x) the resulting
dataframe's columns containing the methylation data (coverage#, numCs#,
numTs#) can safely be renamed using the vector of sampleIDs that I extract
using getSampleID(meth_unite_10x)? Or is there a methylKit function that
does that for me that I've overlooked?
—
Reply to this email directly, view it on GitHub
<#283 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ADK7JDZEPA6MBH6YN7K5T2DXGU4WJANCNFSM6AAAAAAYCT7DYE>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.The text was updated successfully, but these errors were encountered: