Specify platform for readIDATpair()
alanlamsiu opened this issue · comments
Hi @zwdzwd,
I was trying to read the idat files for a set of EPICv2 samples using the following.
sigdf_raw=lapply(searchIDATprefixes("../idat/"), readIDATpair, platform="EPICv2")
Then I used bisConversionControl() for getting the bisulfite conversion rate.
do.call(rbind, lapply(sigdf_raw, bisConversionControl))
But it showed an error as below.
It seems that EPICv2 is not supported in bisConversionControl(). Is there way to get sesame work with EPICv2?
Thanks.
Please see sessionInfo() output below.
R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /sc/arion/work/linx19/conda_envs/sesame_v1.20.0/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0
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
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] planet_1.10.0 scales_1.3.0
[3] wheatmap_0.2.0 ggrepel_0.9.4
[5] ggplot2_3.4.4 pals_1.8
[7] tidyr_1.3.0 dplyr_1.1.4
[9] SummarizedExperiment_1.32.0 Biobase_2.62.0
[11] GenomicRanges_1.54.1 GenomeInfoDb_1.38.5
[13] IRanges_2.36.0 S4Vectors_0.40.2
[15] MatrixGenerics_1.14.0 matrixStats_1.2.0
[17] sesame_1.20.0 sesameData_1.20.0
[19] ExperimentHub_2.10.0 AnnotationHub_3.10.0
[21] BiocFileCache_2.10.1 dbplyr_2.4.0
[23] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] DBI_1.2.0 bitops_1.0-7
[3] rlang_1.1.2 magrittr_2.0.3
[5] compiler_4.3.2 RSQLite_2.3.4
[7] maps_3.4.2 png_0.1-8
[9] vctrs_0.6.5 reshape2_1.4.4
[11] stringr_1.5.1 pkgconfig_2.0.3
[13] crayon_1.5.2 fastmap_1.1.1
[15] XVector_0.42.0 ellipsis_0.3.2
[17] labeling_0.4.3 utf8_1.2.4
[19] promises_1.2.1 tzdb_0.4.0
[21] preprocessCore_1.64.0 purrr_1.0.2
[23] bit_4.0.5 zlibbioc_1.48.0
[25] cachem_1.0.8 jsonlite_1.8.8
[27] blob_1.2.4 later_1.3.2
[29] DelayedArray_0.28.0 uuid_1.1-1
[31] BiocParallel_1.36.0 interactiveDisplayBase_1.40.0
[33] parallel_4.3.2 R6_2.5.1
[35] stringi_1.8.3 RColorBrewer_1.1-3
[37] Rcpp_1.0.11 IRkernel_1.3.2
[39] base64enc_0.1-3 readr_2.1.4
[41] illuminaio_0.44.0 httpuv_1.6.13
[43] Matrix_1.6-4 tidyselect_1.2.0
[45] dichromat_2.0-0.1 abind_1.4-5
[47] yaml_2.3.8 codetools_0.2-19
[49] curl_5.2.0 lattice_0.22-5
[51] tibble_3.2.1 plyr_1.8.9
[53] withr_2.5.2 shiny_1.8.0
[55] KEGGREST_1.42.0 askpass_1.2.0
[57] evaluate_0.23 Biostrings_2.70.1
[59] pillar_1.9.0 BiocManager_1.30.22
[61] filelock_1.0.3 KernSmooth_2.23-22
[63] generics_0.1.3 RCurl_1.98-1.13
[65] IRdisplay_1.1 BiocVersion_3.18.1
[67] hms_1.1.3 munsell_0.5.0
[69] xtable_1.8-4 glue_1.6.2
[71] mapproj_1.2.11 tools_4.3.2
[73] pbdZMQ_0.3-10 grid_4.3.2
[75] base64_2.0.1 AnnotationDbi_1.64.1
[77] colorspace_2.1-0 GenomeInfoDbData_1.2.11
[79] repr_1.1.6 cli_3.6.2
[81] rappdirs_0.3.3 fansi_1.0.6
[83] S4Arrays_1.2.0 gtable_0.3.4
[85] digest_0.6.33 SparseArray_1.2.3
[87] farver_2.1.1 memoise_2.0.1
[89] htmltools_0.5.7 lifecycle_1.0.4
[91] httr_1.4.7 mime_0.12
[93] MASS_7.3-60 openssl_2.1.1
[95] bit64_4.0.5
Dear alanlamsiu,
I have had a similar issue for bisConversionControl for EPICv2. Zhou came up with a solution that worked for me even though I had to create an object from openSesame() with "EPIC" as input.
Best,
Steffan
@SteffanChristiansen Thanks for pointing to the previous issue. It worked for me as you've suggested to specify the platform as EPIC.
Sorry for late reply. With version 1.18+, one shouldn't need to set the platform to EPIC with EPICv2 data. The following code should work
Line 527 in b6abdbc
for bisConversionControl
One can swap the "EPICv2" for other platform that is being used too.