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. It also maintains probe annotation for different Infinium platforms.

Load sesameData

library(sesameData)

Caching data on local disk

Each datum is accessible through the sesameDataGet interface which allows package level in-memory caching. 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(): 2021-04-22
## [1] TRUE

or choose to cache all sesame data, by

sesameDataCacheAll()

Retrieval data

Then data 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()
##              EPIC.1.LNCaP             EPIC.5.normal        EPIC.hg19.manifest 
##                  "EH3659"                  "EH3660"                  "EH3670" 
##        EPIC.hg38.manifest            EPIC.probeInfo           leukocyte.betas 
##                  "EH3671"                  "EH3676"                  "EH3679" 
##           ref.methylation             age.inference       ethnicity.inference 
##                  "EH3680"                  "EH3681"                  "EH3682" 
##             sex.inference           detection.stats           genomeInfo.hg19 
##                  "EH3683"                  "EH3684"                  "EH3665" 
##           genomeInfo.hg38 HM450.10.TCGA.PAAD.normal HM450.10.TCGA.BLCA.normal 
##                  "EH3666"                  "EH3662"                  "EH3663" 
##     HM450.76.TCGA.matched       HM450.hg19.manifest       HM450.hg38.manifest 
##                  "EH3664"                  "EH3674"                  "EH3675" 
##           HM450.probeInfo           leukocyte.betas           ref.methylation 
##                  "EH3677"                  "EH3679"                  "EH3680" 
##             age.inference       ethnicity.inference             sex.inference 
##                  "EH3681"                  "EH3682"                  "EH3683" 
##           detection.stats           genomeInfo.hg19           genomeInfo.hg38 
##                  "EH3684"                  "EH3665"                  "EH3666" 
##        HM27.hg19.manifest        HM27.hg38.manifest            HM27.probeInfo 
##                  "EH3672"                  "EH3673"                  "EH3678" 
##           genomeInfo.hg19           genomeInfo.hg38 
##                  "EH3665"                  "EH3666"

Download .tsv.gz from the annotation website

mft <- sesameDataGetAnno("HM27/HM27.hg19.manifest.tsv.gz")
## Retrieving manifest from  http://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 manifest from  http://zhouserver.research.chop.edu//InfiniumAnnotation/current/EPIC/EPIC.hg19.typeI_overlap_b151.rds ... Done.