Probe missing from Manifest of HM450 and EPIC

[hsun3163]

Hi Wanding, thank you for developing the package in place of Minfi.

I have encountered an error trying to annotate the methylation data:

While analyzing a dataset for HM450 Human methylation, the following error occurs:

Error: subscript contains invalid names

After a manual binary search, one of the problematic probes is "cg01238044"

> sesameData::sesameData_annoProbes("cg01238044",platform = "HM450")
Error: subscript contains invalid names

As it turns out, this probe is not in the Manifest of EPIC and HM450

> sesameData_getManifestGRanges("EPIC")["cg01238044"]
Error: subscript contains invalid names
> sesameData_getManifestGRanges("HM450")["cg01238044"]
Error: subscript contains invalid names

The sessionInfo is as followed:

R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
[1] C

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

other attached packages:
[1] sesame_1.14.2       sesameData_1.14.0   ExperimentHub_2.4.0
[4] AnnotationHub_3.4.0 BiocFileCache_2.4.0 dbplyr_2.2.1
[7] BiocGenerics_0.42.0

loaded via a namespace (and not attached):
 [1] bitops_1.0-7                  matrixStats_0.62.0
 [3] bit64_4.0.5                   filelock_1.0.2
 [5] RColorBrewer_1.1-3            httr_1.4.3
 [7] GenomeInfoDb_1.32.3           tools_4.2.0
 [9] utf8_1.2.2                    R6_2.5.1
[11] DBI_1.1.3                     colorspace_2.0-3
[13] tidyselect_1.1.2              base64_2.0
[15] bit_4.0.4                     curl_4.3.2
[17] compiler_4.2.0                preprocessCore_1.58.0
[19] cli_3.3.0                     Biobase_2.56.0
[21] DelayedArray_0.22.0           scales_1.2.0
[23] readr_2.1.2                   askpass_1.1
[25] rappdirs_0.3.3                stringr_1.4.0
[27] digest_0.6.29                 illuminaio_0.38.0
[29] XVector_0.36.0                pkgconfig_2.0.3
[31] htmltools_0.5.3               MatrixGenerics_1.8.1
[33] fastmap_1.1.0                 rlang_1.0.2
[35] RSQLite_2.2.15                shiny_1.7.1
[37] generics_0.1.3                wheatmap_0.2.0
[39] BiocParallel_1.30.3           dplyr_1.0.9
[41] RCurl_1.98-1.7                magrittr_2.0.3
[43] GenomeInfoDbData_1.2.8        Matrix_1.4-1
[45] Rcpp_1.0.9                    munsell_0.5.0
[47] S4Vectors_0.34.0              fansi_1.0.3
[49] lifecycle_1.0.1               stringi_1.7.6
[51] yaml_2.3.5                    MASS_7.3-56
[53] SummarizedExperiment_1.26.1   zlibbioc_1.42.0
[55] plyr_1.8.7                    grid_4.2.0
[57] blob_1.2.3                    parallel_4.2.0
[59] promises_1.2.0.1              crayon_1.5.1
[61] lattice_0.20-45               Biostrings_2.64.0
[63] hms_1.1.1                     KEGGREST_1.36.3
[65] pillar_1.7.0                  GenomicRanges_1.48.0
[67] reshape2_1.4.4                codetools_0.2-18
[69] stats4_4.2.0                  glue_1.6.2
[71] BiocVersion_3.15.2            BiocManager_1.30.18
[73] png_0.1-7                     vctrs_0.4.1
[75] tzdb_0.3.0                    httpuv_1.6.5
[77] gtable_0.3.0                  openssl_2.0.2
[79] purrr_0.3.4                   assertthat_0.2.1
[81] cachem_1.0.6                  ggplot2_3.3.6
[83] mime_0.12                     xtable_1.8-4
[85] later_1.3.0                   tibble_3.1.7
[87] AnnotationDbi_1.58.0          memoise_2.0.1
[89] IRanges_2.30.0                ellipsis_0.3.2
[91] interactiveDisplayBase_1.34.0

[zwdzwd]

Thanks for reporting. This is due to the probe being mapped to a decoy contig in hg38. We will need to update the manifest so we don't lose any probes in the manifest GRanges. For now, I added a check (v1.15.1) to exclude such probes from the annotation instead of causing the code to abort.