sesameData User Guide

Installation

From Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("sesameData")

Development version can be installed from github

library(devtools)
install_github('zwdzwd/sesameData')

Usage

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.

Load 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 the examples.

## snapshotDate(): 2022-01-20
## Metadata (N=6):

or 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.

Retrieval data

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

List available data

Titles of all the available data can be shown with:

## # A tibble: 93 × 2
##    EHID  Title               
##    <chr> <chr>               
##  1 TBD   EPIC.1.SigDF        
##  2 TBD   EPIC.address        
##  3 TBD   EPIC.addressSpecies 
##  4 TBD   EPIC.publicQC       
##  5 TBD   EPIC.tissueSignature
##  6 TBD   genomeInfo.hg19     
##  7 TBD   genomeInfo.hg38     
##  8 TBD   genomeInfo.mm10     
##  9 TBD   HM450.addressSpecies
## 10 TBD   HM450.address       
## # … with 83 more rows

Download .tsv.gz from the annotation website

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

Download RDS files from the annotation website

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

Download annotation file to disk

## $url
## [1] "https://zhouserver.research.chop.edu/sesameData/raw/3999492009_R01C01_Grn.idat"
## 
## $dest_dir
## [1] "/tmp/Rtmpc5dAjC"
## 
## $dest_file
## [1] "/tmp/Rtmpc5dAjC/3999492009_R01C01_Grn.idat"
## 
## $file_name
## [1] "3999492009_R01C01_Grn.idat"
## R Under development (unstable) (2022-01-05 r81451)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.15-data-experiment/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.15-data-experiment/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] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] GenomicRanges_1.47.6 GenomeInfoDb_1.31.2  IRanges_2.29.1      
##  [4] S4Vectors_0.33.10    sesameData_1.13.13   rmarkdown_2.11      
##  [7] ExperimentHub_2.3.5  AnnotationHub_3.3.8  BiocFileCache_2.3.4 
## [10] dbplyr_2.1.1         BiocGenerics_0.41.2 
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.8                    png_0.1-7                    
##  [3] Biostrings_2.63.1             assertthat_0.2.1             
##  [5] digest_0.6.29                 utf8_1.2.2                   
##  [7] mime_0.12                     R6_2.5.1                     
##  [9] RSQLite_2.2.9                 evaluate_0.14                
## [11] httr_1.4.2                    pillar_1.6.4                 
## [13] zlibbioc_1.41.0               rlang_0.4.12                 
## [15] curl_4.3.2                    jquerylib_0.1.4              
## [17] blob_1.2.2                    stringr_1.4.0                
## [19] RCurl_1.98-1.5                bit_4.0.4                    
## [21] shiny_1.7.1                   compiler_4.2.0               
## [23] httpuv_1.6.5                  xfun_0.29                    
## [25] pkgconfig_2.0.3               htmltools_0.5.2              
## [27] tidyselect_1.1.1              KEGGREST_1.35.0              
## [29] tibble_3.1.6                  GenomeInfoDbData_1.2.7       
## [31] interactiveDisplayBase_1.33.0 fansi_1.0.2                  
## [33] withr_2.4.3                   crayon_1.4.2                 
## [35] dplyr_1.0.7                   later_1.3.0                  
## [37] bitops_1.0-7                  rappdirs_0.3.3               
## [39] jsonlite_1.7.3                xtable_1.8-4                 
## [41] lifecycle_1.0.1               DBI_1.1.2                    
## [43] magrittr_2.0.1                cli_3.1.1                    
## [45] stringi_1.7.6                 cachem_1.0.6                 
## [47] XVector_0.35.0                promises_1.2.0.1             
## [49] bslib_0.3.1                   ellipsis_0.3.2               
## [51] filelock_1.0.2                generics_0.1.1               
## [53] vctrs_0.3.8                   tools_4.2.0                  
## [55] bit64_4.0.5                   Biobase_2.55.0               
## [57] glue_1.6.1                    purrr_0.3.4                  
## [59] BiocVersion_3.15.0            fastmap_1.1.0                
## [61] yaml_2.2.1                    AnnotationDbi_1.57.1         
## [63] BiocManager_1.30.16           memoise_2.0.1                
## [65] knitr_1.37                    sass_0.4.0