queryTME: A function to query TME datasets available in this package

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

A function to query TME datasets available in this package

Description

This function allows you to search and subset included TME datasets. A list of tme_data objects matching the provided options will be returned, if queryTME is called without any options it will retrieve all available datasets. This should only be done on machines with a large amount of ram (>64gb) because some datasets are quite large. In most cases it is recommended to instead filter databases with some criteria.

Usage

queryTME(
  geo_accession = NULL,
  score_type = NULL,
  has_signatures = NULL,
  has_truth = NULL,
  tumour_type = NULL,
  author = NULL,
  journal = NULL,
  year = NULL,
  pmid = NULL,
  sequence_tech = NULL,
  organism = NULL,
  metadata_only = FALSE,
  sparse = FALSE
)

Arguments

geo_accession	Search by geo accession number. Good for returning individual datasets
score_type	Search by type of score (TPM, FPKM, raw count)
has_signatures	Return only those datasets that have cell-type gene signatures available, or only those without (TRUE/FALSE)
has_truth	Return only those datasets that have cell-type annotations available, or only those without annotations
tumour_type	Search by type of tumour represented by the dataset
author	Search by the author who published the dataset
journal	Search by the journal the dataset was published in.
year	Search by exact year or year ranges with '<', '>', or '-'. For example, you can return datasets newer than 2013 with '>2013'
pmid	Search by Pubmed ID associated with the study. Good for returning individual datasets
sequence_tech	Search by sequencing technology used to sample the cells.
organism	Search by source organism used in the study, for example human or mouse.
metadata_only	Return rows of metadata instead of actual datasets. Useful for exploring what data is available without actually downloading data. Defaults to FALSE
sparse	Return expression as a sparse matrix. Uses less memory but is less convenient to view, recommended only if encounter memory issues with dense data. Defaults to FALSE.

Value

A list containing a table of metadata or one or more SingleCellExperiment objects

Examples

## Retrieve the metadata table to see what data is available
res <- queryTME(metadata_only = TRUE)

## Retrieve a filtered metadata table that only shows datasets with 
## cell type annotations and cell type gene signatures
res <- queryTME(has_truth = TRUE, has_signatures = TRUE, metadata_only = TRUE)

## Retrieve a single dataset identified from the table
res <- queryTME(geo_accession = "GSE72056")

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