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Table 1 A catalog of ReUseData functions

From: ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management

Category

Function

Description

data recipe

recipeMake

Create data recipe from scratch or existing shell script

recipeUpdate

Synchronize and update the data recipes GitHub repository or user-specified private GitHub repository

recipeSearch

Search existing data recipes in the cache path of "recipeUpdate"

recipeLoad

Load one or more data recipes into the R environment

recipeNames

S4 method for "recipeHub" object (data recipe representation in R). Returns the recipe name(s)

getData

Evaluation of data recipe to generate curate data file(s) of interest

Curated data

dataUpdate

Function to update the local data records by reading the yaml files in the specified directory recursively

dataSearch

Search specific data files in the local data caching system using one or more keywords

dataNames

S4 method for "dataHub" object (data files representation in R). Returns the name(s) of data files

dataNotes

S4 method for "dataHub" object. Returns the "notes" of the data that was defined in "getData"

dataParams

S4 method for "dataHub" object. Returns the input parameter values for the corresponding data recipe

dataPaths

S4 method for "dataHub" object. Returns the file path(s) of corresponding data files

dataTags

S4 method for "dataHub" object. Returns the tags of data files (if exist)

dataTags < -

Function to assign a string tag to specific data files

dataYml

S4 method for "dataHub" object. Returns the yaml file path(s) for corresponding data file(s)

getCloudData

Download the pre-generated curated data sets from ReUseData Google Cloud Bucket