In Bishop-Laboratory/RLHub: An ExperimentHub package for accessing processed RLSuite data sets

Introduction

RLHub ("R-Loop Hub") provides processed data sets for the RLSuite toolchain. It is an ExperimentHub package containing annotations of R-Loop consensus regions, genomic features directly relevant to R-loops, such as R-loop-forming sequences (RLFS), G-or-C skew regions, and other data of relevance to RLSuite.

All data were generated via the protocol in the RLBase-data repository.

Installation

RLHub can be installed from Bioconductor via the following command:

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

BiocManager::install("RLHub")

RLHub may also be installed from GitHub:

remotes::install_github("Bishop-Laboratory/RLHub")

Accessing RLHub Data

library(RLHub)

Data can be conveniently accessed through ExperimentHub functions or with the built-in accessors available through RLHub.

A summary of the data can also be found by running the following:

?`RLHub-package`

The full manifest of the available data is found here:

DT::datatable(
    read.csv(system.file("extdata", "metadata.csv", package = "RLHub")),
    options = list(
        scrollX=TRUE,
        pageLength = 5
    )
)

The Tags column list the function names used to access each data set. This method of access is detailed below.

Built-in functions

In the below example, we show how one can access data using convenient built-in functions.

# Access the R-loop binding proteins (RLBPs) data set
rlbps <- RLHub::rlbps()
DT::datatable(rlbps)

The data access function name is simply the value in Tags corresponding to the entry for that data set in the metadata.csv table. In this example,"rlbps" is the tag corresponding to entry #5: "R-loop-binding proteins discovered from mass-spec studies." Therefore, the function to access this data is simply RLHub::rlbps().

For examples of all accessors, please run the following:

?`RLHub-package`

ExperimentHub objects

library(ExperimentHub)

In this example, we show how to access RLHub data using the ExperimentHub object.

eh <- ExperimentHub()
rlhub <- query(eh, "RLHub")
rlhub

If we want to obtain the R-loop-binding proteins, for example, we can do so with corresponding ExperimentHub ID.

rlbps <- rlhub[["EH6797"]]
DT::datatable(rlbps)

Finally, all package resources may be loaded as a list using loadResources().

rlhublst <- loadResources(rlhub, package = "RLHub")
names(rlhublst) <- listResources(rlhub, package = "RLHub")

Session info

sessionInfo()

Bishop-Laboratory/RLHub documentation built on Jan. 20, 2022, 3:47 p.m.