FASTGenomics/fgread-r

R readers for different data formats for FASTGenomics.

FASTGenomics Reader Module for R

This package implements convenience functions for loading datasets in the FASTGenomics analysis environment. The functions from this package will let you list and load datasets for which the analysis was defined.

Documentation

For the general documentation on how to use the reader, please visit our FASTGenomics Documentation.

For details on the available functions see the API Documentation.

Limitations

TSV/CSV Reader

Loading large files, especially if they are very sparse, in plain text format need a lot of memory and can be rather slow. For large datasets we recommend to use formats that support sparse data.

AnnData Reader

As the internal Seurat reader for AnnData fails to convert certain datasets (depending on scaling, normalization etc.), we provide a custom reader. This custom reader, however, only reads the .X, .obs and .var components of the AnnData object.

Known issues

Please report the issues through github.

Development and testing

Clone the repository along with the test data by running

git clone --recurse-submodules git@github.com:FASTGenomics/fgread-r.git

Then enter the fgread-r directory and install the dependencies with

install.packages("devtools")
devtools::install_deps(upgrade="never")

To test the package use

devtools::test()

Build Documentaion

devtools::document()