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 a specific assay platform, say HM27 by

## snapshotDate(): 2021-10-06
## [1] TRUE

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:

##              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"

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/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