spaceRATScaffolds

This package contains scaffolds used for spaceRAT. See the package vignettes for instructions how to build and use the scaffolds.

Installation

Install from GitHub

# Install using remotes
# install.packages("remotes")
remotes::install_github("shdam/spaceRATScaffolds", build_vignettes = TRUE)

Usage

This is a data package. The current spaceRAT scaffolds include:

library("spaceRATScaffolds")

listScaffolds()
#> [1] "TCGA.v2" "DMAP.v1" "GTEx.v1" "TCGA.v1"

listDatasets()
#> [1] "DMAP_exprs"    "DMAP_pData"    "ilaria_counts" "ilaria_pData"

listConverters()
#> [1] "gene_id_converter_hs" "gene_id_converter_mm"

Get scaffold

scaffold <- getScaffold("DMAP")

# Add versioning to get a specific version:
scaffold.v1 <- getScaffold("DMAP.v1", store = TRUE, path = "scaffolds")

If you set store = TRUE, the scaffold will be stored locally in the folder set by path. When re-acquiring the scaffold, getScaffold("DMAP.v1", path = "scaffolds") will load the local scaffold instead of downloading from Zenodo.

Load test data

# Load test data 
testData <- loadData("DMAP_exprs")
testPheno <- loadData("DMAP_pData")

Using spaceRAT

See spaceRAT for instructions on how to use the scaffolds.

Report issues

If you have any issues or questions regarding the use of spaceRATScaffolds, please do not hesitate to raise an issue on GitHub. In this way, others may also benefit from the answers and discussions.