BiscuiteerData User Guide

Package

biscuiteerData 1.6.0

1 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.

2 Quick Start

2.1 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")

3 Usage

biscuiteerData data is accessible using the biscuiteerDataGet function:

library(biscuiteerData)

## 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.max, which.min

## Loading required package: AnnotationHub

## Loading required package: BiocFileCache

## Loading required package: dbplyr

## Loading biscuiteerData.

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

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

biscuiteerDataList()

## snapshotDate(): 2021-05-05

## [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()

## snapshotDate(): 2021-05-05

## [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")