From Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("sesameData")Development version can be installed from github
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:
## 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, colMeans, colSums, colnames,
## dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
## intersect, is.unsorted, lapply, lengths, mapply, match, mget,
## order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
## rowMeans, rowSums, rownames, sapply, setdiff, sort, table,
## tapply, union, unique, unsplit, which, which.max, which.min## Loading required package: AnnotationHub## Loading sesameData.Titles of all the available data can be shown with:
## snapshotDate(): 2018-10-31## [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
## snapshotDate(): 2018-10-31## [1] "2018-05-02" "2018-09-19"Retrieve an old version