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.

Each datum is accessible through the sesameDataGet interface which allows package level in-memory caching. For example, data can be retrieved with the title:

library(sesameData)
## Loading required package: ExperimentHub
## Loading required package: BiocGenerics
## Loading required package: parallel
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
## 
##     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
##     clusterExport, clusterMap, parApply, parCapply, parLapply,
##     parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
##     as.data.frame, basename, cbind, colnames, dirname, do.call,
##     duplicated, eval, evalq, get, grep, grepl, intersect,
##     is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
##     pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
##     setdiff, sort, table, tapply, union, unique, unsplit, which,
##     which.max, which.min
## Loading required package: AnnotationHub
## Loading required package: BiocFileCache
## Loading required package: dbplyr
## Loading sesameData.
EPIC.hg38.manifest = sesameDataGet('EPIC.hg38.manifest')

Titles of all the available data can be shown with:

sesameDataList()
## snapshotDate(): 2019-05-07
##  [1] "EPIC.1.LNCaP"              "EPIC.5.normal"            
##  [3] "HM450.1.TCGA.PAAD"         "HM450.10.TCGA.PAAD.normal"
##  [5] "HM450.10.TCGA.BLCA.normal" "HM450.76.TCGA.matched"    
##  [7] "genomeInfo.hg19"           "genomeInfo.hg38"          
##  [9] "EPIC.address"              "HM450.address"            
## [11] "HM27.address"              "EPIC.hg19.manifest"       
## [13] "EPIC.hg38.manifest"        "HM27.hg19.manifest"       
## [15] "HM27.hg38.manifest"        "HM450.hg19.manifest"      
## [17] "HM450.hg38.manifest"       "EPIC.probeInfo"           
## [19] "HM450.probeInfo"           "HM27.probeInfo"           
## [21] "leukocyte.betas"           "ref.methylation"          
## [23] "age.inference"             "ethnicity.inference"      
## [25] "sex.inference"

List all versions

sesameDataListDates()
## snapshotDate(): 2019-05-07
## [1] "2018-05-02" "2018-09-19"

Retrieve an old version

probeInfo.oldversion = sesameDataGet('HM27.probeInfo', dateAdded='2018-05-02')