From Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("sesameData")Development version can be installed from github
sesameData package provides associated data for sesame package. This includes example data for testing and instructional purpose, as we ll as probe annotation for different Infinium platforms.
Each datum is accessible through the sesameDataGet interface. It should be noted that all data must be pre-cached to local disk before they can be used. This design is to prevent conflict in annotation data caching and remove internet dependency. Caching needs only be done once per sesame/sesameData installation. One can cache data for a specific assay platform, say HM27 by
## snapshotDate(): 2021-10-06## [1] TRUEor choose to cache all sesame data, by
Once a data object is loaded, it is stored to a tempoary cache, so that the data doesn’t need to be retrieved again next time we call sesameDataGet. This design is meant to speeed up the run time.
For example, the annotation for HM27 can be retrieved with the title:
Titles of all the available data can be shown with:
## EPIC.address EPIC.1.LNCaP EPIC.5.normal
## "EH5963" "EH3659" "EH3660"
## EPIC.hg19.manifest EPIC.hg38.manifest EPIC.probeInfo
## "EH3670" "EH3671" "EH3676"
## leukocyte.betas ref.methylation age.inference
## "EH3679" "EH3680" "EH3681"
## ethnicity.inference sex.inference detection.stats
## "EH3682" "EH3683" "EH3684"
## genomeInfo.hg19 genomeInfo.hg38 idatSignature
## "EH3665" "EH3666" "EH6018"
## probeIDSignature HM450.address HM450.1.TCGA.PAAD
## "EH6019" "EH5966" "EH5965"
## HM450.10.TCGA.PAAD.normal HM450.10.TCGA.BLCA.normal HM450.76.TCGA.matched
## "EH3662" "EH3663" "EH3664"
## HM450.hg19.manifest HM450.hg38.manifest HM450.probeInfo
## "EH3674" "EH3675" "EH3677"
## leukocyte.betas ref.methylation age.inference
## "EH3679" "EH3680" "EH3681"
## ethnicity.inference sex.inference detection.stats
## "EH3682" "EH3683" "EH3684"
## genomeInfo.hg19 genomeInfo.hg38 idatSignature
## "EH3665" "EH3666" "EH6018"
## probeIDSignature HM27.address HM27.hg19.manifest
## "EH6019" "EH5964" "EH3672"
## HM27.hg38.manifest HM27.probeInfo genomeInfo.hg19
## "EH3673" "EH3678" "EH3665"
## genomeInfo.hg38 idatSignature probeIDSignature
## "EH3666" "EH6018" "EH6019"
## MM285.address MM285.1.NOD.FrontalLobe MM285.10.tissue
## "EH5970" "EH5968" "EH5969"
## MM285.clock347 MM285.mm10.manifest MM285.strain.snp.table
## "EH5971" "EH5972" "EH5973"
## MM285.tissueSignature MM285.bloodSignature idatSignature
## "EH5974" "EH6016" "EH6018"
## probeIDSignature Mammal40.address Mammal40.alignmentScore
## "EH6019" "EH4679" "EH6017"
## idatSignature probeIDSignature
## "EH6018" "EH6019"## Retrieving annotation from https://zhouserver.research.chop.edu/InfiniumAnnotation/current/HM27/HM27.hg19.manifest.tsv.gz ... Done.## Retrieving annotation from https://zhouserver.research.chop.edu/InfiniumAnnotation/current/EPIC/EPIC.hg19.typeI_overlap_b151.rds ... Done.## $url
## [1] "https://zhouserver.research.chop.edu/sesameData/raw/3999492009_R01C01_Grn.idat"
##
## $dest_dir
## [1] "/tmp/Rtmphn8gCe"
##
## $dest_file
## [1] "/tmp/Rtmphn8gCe/3999492009_R01C01_Grn.idat"
##
## $file_name
## [1] "3999492009_R01C01_Grn.idat"## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.13-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.13-bioc/R/lib/libRlapack.so
##
## 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
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] sesameData_1.10.1 rmarkdown_2.11 ExperimentHub_2.0.0
## [4] AnnotationHub_3.0.1 BiocFileCache_2.0.0 dbplyr_2.1.1
## [7] BiocGenerics_0.38.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.7 png_0.1-7
## [3] Biostrings_2.60.2 assertthat_0.2.1
## [5] digest_0.6.28 utf8_1.2.2
## [7] mime_0.12 R6_2.5.1
## [9] GenomeInfoDb_1.28.4 stats4_4.1.1
## [11] RSQLite_2.2.8 evaluate_0.14
## [13] httr_1.4.2 pillar_1.6.3
## [15] zlibbioc_1.38.0 rlang_0.4.11
## [17] curl_4.3.2 jquerylib_0.1.4
## [19] blob_1.2.2 S4Vectors_0.30.2
## [21] stringr_1.4.0 RCurl_1.98-1.5
## [23] bit_4.0.4 shiny_1.7.1
## [25] compiler_4.1.1 httpuv_1.6.3
## [27] xfun_0.26 pkgconfig_2.0.3
## [29] htmltools_0.5.2 tidyselect_1.1.1
## [31] KEGGREST_1.32.0 tibble_3.1.5
## [33] GenomeInfoDbData_1.2.6 interactiveDisplayBase_1.30.0
## [35] IRanges_2.26.0 fansi_0.5.0
## [37] withr_2.4.2 crayon_1.4.1
## [39] dplyr_1.0.7 later_1.3.0
## [41] bitops_1.0-7 rappdirs_0.3.3
## [43] jsonlite_1.7.2 xtable_1.8-4
## [45] lifecycle_1.0.1 DBI_1.1.1
## [47] magrittr_2.0.1 stringi_1.7.5
## [49] cachem_1.0.6 XVector_0.32.0
## [51] promises_1.2.0.1 bslib_0.3.0
## [53] ellipsis_0.3.2 filelock_1.0.2
## [55] generics_0.1.0 vctrs_0.3.8
## [57] tools_4.1.1 bit64_4.0.5
## [59] Biobase_2.52.0 glue_1.4.2
## [61] purrr_0.3.4 BiocVersion_3.13.1
## [63] fastmap_1.1.0 yaml_2.2.1
## [65] AnnotationDbi_1.54.1 BiocManager_1.30.16
## [67] memoise_2.0.0 knitr_1.36
## [69] sass_0.4.0