Load sesameData

library(sesameData)

Caching data on local disk

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

sesameDataCache("HM27")

## snapshotDate(): 2021-10-18

## [1] TRUE

or choose to cache all sesame data, by

sesameDataCacheAll()

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.

Retrieval data

For example, the annotation for HM27 can be retrieved with the title:

HM27.hg38.manifest = sesameDataGet('HM27.hg38.manifest')

List available data

Titles of all the available data can be shown with:

sesameDataList()

## # A tibble: 70 × 2
##    EHID   Title                             
##    <chr>  <chr>                             
##  1 EH6809 KYCG.EPIC.CGI.20210713            
##  2 EH6810 KYCG.EPIC.chromosome.hg19.20210630
##  3 EH6811 KYCG.EPIC.chromosome.hg38.20210630
##  4 EH6812 KYCG.EPIC.gene.20210923           
##  5 EH6813 KYCG.EPIC.histoneMod.20210819     
##  6 EH6814 KYCG.EPIC.mask.hg19.20181001      
##  7 EH6815 KYCG.EPIC.mask.hg38.20181001      
##  8 EH6816 KYCG.EPIC.probeType.20210630      
##  9 EH6817 KYCG.EPIC.seqContext.20210713     
## 10 EH6818 KYCG.EPIC.TFBS.20210817           
## # … with 60 more rows

Download .tsv.gz from the annotation website

mft <- sesameDataGetAnno("HM27/HM27.hg19.manifest.tsv.gz")

## Retrieving annotation from  https://zhouserver.research.chop.edu/InfiniumAnnotation/current/HM27/HM27.hg19.manifest.tsv.gz ... Done.

Download RDS files from the annotation website

annoS <- sesameDataGetAnno("EPIC/EPIC.hg19.typeI_overlap_b151.rds")

## Retrieving annotation from  https://zhouserver.research.chop.edu/InfiniumAnnotation/current/EPIC/EPIC.hg19.typeI_overlap_b151.rds ... Done.

Download annotation file to disk

sesameDataDownload("3999492009_R01C01_Grn.idat", dest_dir = tempdir())

## $url
## [1] "https://zhouserver.research.chop.edu/sesameData/raw/3999492009_R01C01_Grn.idat"
## 
## $dest_dir
## [1] "/tmp/Rtmpqvbnjf"
## 
## $dest_file
## [1] "/tmp/Rtmpqvbnjf/3999492009_R01C01_Grn.idat"
## 
## $file_name
## [1] "3999492009_R01C01_Grn.idat"

sessionInfo()

## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] sesameData_1.12.0   rmarkdown_2.11      ExperimentHub_2.2.0
## [4] AnnotationHub_3.2.0 BiocFileCache_2.2.0 dbplyr_2.1.1       
## [7] BiocGenerics_0.40.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.7                    png_0.1-7                    
##  [3] Biostrings_2.62.0             assertthat_0.2.1             
##  [5] digest_0.6.28                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] GenomeInfoDb_1.30.0           stats4_4.1.1                 
## [11] RSQLite_2.2.8                 evaluate_0.14                
## [13] httr_1.4.2                    pillar_1.6.4                 
## [15] zlibbioc_1.40.0               rlang_0.4.12                 
## [17] curl_4.3.2                    jquerylib_0.1.4              
## [19] blob_1.2.2                    S4Vectors_0.32.0             
## [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_0.27                     pkgconfig_2.0.3              
## [29] htmltools_0.5.2               tidyselect_1.1.1             
## [31] KEGGREST_1.34.0               tibble_3.1.5                 
## [33] GenomeInfoDbData_1.2.7        interactiveDisplayBase_1.32.0
## [35] IRanges_2.28.0                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                cli_3.1.0                    
## [49] stringi_1.7.5                 cachem_1.0.6                 
## [51] XVector_0.34.0                promises_1.2.0.1             
## [53] bslib_0.3.1                   ellipsis_0.3.2               
## [55] filelock_1.0.2                generics_0.1.1               
## [57] vctrs_0.3.8                   tools_4.1.1                  
## [59] bit64_4.0.5                   Biobase_2.54.0               
## [61] glue_1.4.2                    purrr_0.3.4                  
## [63] BiocVersion_3.14.0            fastmap_1.1.0                
## [65] yaml_2.2.1                    AnnotationDbi_1.56.1         
## [67] BiocManager_1.30.16           memoise_2.0.0                
## [69] knitr_1.36                    sass_0.4.0