This package provides the manifest for the Illumina Human Methylation MSA array, based on the csv available on their support site .
The script used to generate the manifest can be found in /tmp/RtmpdwrudD/Rinst28af64617540/IlluminaHumanMethylationMSAmanifest/scripts/manifest.R.
Curently minfi will not automatically identify the array correctly, so this must be set by hand. As an example:
RGset <- read.metharray.exp(...)
annotation(RGset) <- list(array = "IlluminaHumanMethylationMSA",
annotation = "20a1.hg38")After setting the annotation, you can then process the RGset as normal.
sessionInfo()## R version 4.4.1 Patched (2024-08-16 r87026)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.5 LTS
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## Matrix products: default
## BLAS: /home/lorikern/R-Installs/bin/R-4-4-branch/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
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## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [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
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## time zone: America/New_York
## tzcode source: system (glibc)
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] knitr_1.48
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## loaded via a namespace (and not attached):
## [1] digest_0.6.37 R6_2.5.1 fastmap_1.2.0 xfun_0.47
## [5] cachem_1.1.0 htmltools_0.5.8.1 rmarkdown_2.28 lifecycle_1.0.4
## [9] cli_3.6.3 sass_0.4.9 jquerylib_0.1.4 compiler_4.4.1
## [13] tools_4.4.1 evaluate_0.24.0 bslib_0.8.0 yaml_2.3.10
## [17] rlang_1.1.4 jsonlite_1.8.8