BiscuiteerData

biscuiteerData is a complementary package to the Bioconductor package biscuiteer. It contains a handful of datasets to be used when running functions in biscuiteer.

Quick Start

Installing

From Bioconductor,

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

A development version is available on GitHub and can be installed via:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("trichelab/biscuiteerData")

Usage

Loading the library for the first time should cache the associated data files. After the initial library load, future loads will skip the cache step.

library(biscuiteerData)
## Loading required package: ExperimentHub
## Loading required package: BiocGenerics
## Loading required package: generics
## 
## Attaching package: 'generics'
## The following objects are masked from 'package:base':
## 
##     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
##     setequal, union
## 
## Attaching package: 'BiocGenerics'
## 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, aperm, append,
##     as.data.frame, basename, cbind, colnames, dirname, do.call,
##     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
##     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
##     unsplit, which.max, which.min
## Loading required package: AnnotationHub
## Loading required package: BiocFileCache
## Loading required package: dbplyr
## Loading biscuiteerData.

biscuiteerData data is accessible using the biscuiteerDataGet function:

PMDs.hg19 <- biscuiteerDataGet("PMDs.hg19.rda")

A list of the titles for the available data can be retrieved via:

biscuiteerDataList()
## [1] "Zhou_solo_WCGW_inCommonPMDs.hg19.rda"
## [2] "PMDs.hg19.rda"                       
## [3] "Zhou_solo_WCGW_inCommonPMDs.hg38.rda"
## [4] "PMDs.hg38.rda"

A list of all versions (where the versions are the dates uploaded) is produced via:

biscuiteerDataListDates()
## [1] "2019-09-25"

An older version of the data can be retrieved using the dateAdded argument of biscuiteerDataGet:

PMDs.hg19 <- biscuiteerDataGet("PMDs.hg19.rda", dateAdded = "2019-09-25")