inst/doc/biscuiteerData.md

In jamorrison/biscuiteerData: Data Package for Biscuiteer

title: "BiscuiteerData User Guide" data: "25 September 2019" package: "biscuiteerData 0.99.0" output: BiocStyle::html_document: highlight: pygments toc_float: true fig_width: 8 fig_height: 6 vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteIndexEntry{Biscuiteer User Guide} %\VignetteEncoding[utf8]{inputenc}

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

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':
## 
##     anyDuplicated, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter,
##     Find, get, grep, grepl, intersect, is.unsorted, lapply, Map,
##     mapply, match, mget, order, paste, pmax, pmax.int, pmin,
##     pmin.int, Position, rank, rbind, Reduce, 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 biscuiteerData.

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

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

biscuiteerDataList()

## snapshotDate(): 2019-09-25

## [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(): 2019-09-25

## [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")

jamorrison/biscuiteerData documentation built on Nov. 4, 2019, 2:17 p.m.