saveTME: A function to save a TME dataset

In shooshtarilab/TMExplorer: A Collection of Tumour Microenvironment Single-cell RNA Sequencing Datasets and Corresponding Metadata

A function to save a TME dataset

Description

This function allows you to save the expression, labels, and cell types to disk in csv format. It takes two options: an object to save and a directory to save in. Multiple files will be created in the provided output directory, one for each type of data available in the tme_data object (expression, gene signatures, cell type annotations).

Usage

saveTME(object, outdir)

Arguments

object	The tme_data object to be written to disk, this should be an individual dataset returned by queryTME.
outdir	The directory to save the tme_data in, the directory should not exist yet.

Value

Nothing

Examples

# Retrieve a previously identified dataset (see queryTME) and save it to disk
res <- queryTME(geo_accession = 'GSE72056')[[1]]
 
saveTME(res, output_directory_name)

shooshtarilab/TMExplorer documentation built on June 7, 2022, 1:31 p.m.