This R package provides a simple function to query GTEx (v8) for gene expression levels, using a set of human gene symbols and a particular tissue type as its main arguments. The function utilizes the GTEx API to retrieve the data. A brief example:
devtools::install_github('sigven/gtexRNA')
exp_dist_gtex <- gtexRNA::get_tpm_data(genes = c('KRAS','BRAF'), tissue_type = 'Bladder')
exp_dist_gtex is a data.frame with all gene expression levels pr. sample, provided with TPM and log2(TPM + 1).
To see the available types of tissues that can be queried, explore the metadata file:
unique(gtexRNA::sampleMetadata$tissue_site_detail_id)
PS: We have not yet found a way to retrieve the actual sample identifiers from the API method, so get_tpm_data() will currently thus return sample records without any sample identifiers.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.