hpaDownload: Download datasets

In trannhatanh89/HPAanalyze: Retrieve and analyze data from the Human Protein Atlas

Download datasets

Description

Download the latest version of HPA datasets and import them in R. It is recommended to only download the datasets you need, as some of them may be very big.

Usage

hpaDownload(downloadList = "histology", version = "latest")

Arguments

downloadList

A vector or string indicate which datasets to download. Possible value: 'Normal tissue' 'Pathology' 'Subcellular location' 'RNA consensus tissue' 'RNA HPA tissue' 'RNA GTEx tissue' 'RNA FANTOM tissue' 'RNA single cell type' 'RNA single cell type tissue cluster' 'RNA GTEx brain region' 'RNA FANTOM brain region' 'RNA pig brain region' 'RNA pig brain subregion sample' 'RNA mouse brain region' 'RNA mouse brain subregion sample' 'RNA Allen mouse brain region' 'RNA HPA immune cell' 'RNA HPA immune cell sample' 'RNA Monaco immune cell' 'RNA Schmiedel immune cell' 'RNA HPA blood cell' (version 21.1) 'RNA HPA blood cell sample' (version 21.1) 'RNA Monaco blood cell' (version 21.1) 'RNA Schmiedel blood cell' (version 21.1) 'RNA HPA cell line cancer' 'RNA HPA cell line' 'RNA TCGA cancer sample' 'RNA transcript tissue' 'RNA transcript GTEx retina' 'RNA transcript immune cells' 'RNA transcript cell line' (version 21.1) 'RNA transcript pig brain' 'RNA transcript mouse brain' You can also use the following shortcuts: 'all': download everything 'histology': same as c('Normal tissue', 'Pathology', 'Subcellular location') 'rna tissue': same as c('RNA consensus tissue', 'RNA HPA tissue', 'RNA GTEx tissue', 'RNA FANTOM tissue') 'rna cell type': same as c('RNA single cell type', 'RNA single cell type tissue cluster') 'rna brain region': same as c('RNA GTEx brain region', 'RNA FANTOM brain region', 'RNA pig brain region', 'RNA pig brain subregion sample', 'RNA mouse brain region', 'RNA mouse brain subregion sample', 'RNA Allen mouse brain region') 'rna immune cell': same as c('RNA HPA immune cell', 'RNA HPA immune cell sample', 'RNA Monaco immune cell', 'RNA Schmiedel immune cell') 'rna blood cell': same as c('RNA HPA blood cell', 'RNA HPA blood cell sample', 'RNA Monaco blood cell', 'RNA Schmiedel blood cell') 'isoform': same as c('RNA transcript tissue', 'RNA transcript GTEx retina', 'RNA transcript immune cells', 'RNA transcript cell line', 'RNA transcript pig brain', 'RNA transcript mouse brain') See https://www.proteinatlas.org/about/download for more information.

version

A string indicate which version to be downloaded. Possible value: 'latest': Download latest version. Certain legacy datasets will be downloaded with the highest version available. Require Internet connection. This is the default option. 'example' or 'built-in': Load the built-in histology dataset from 'HPAanalyze' ('hpa_histology_data'). Do not require internet connection.

Value

This function will return a list of tibbles corresponding to requested datasets.

See Also

hpaDownload hpa_histology_data

Other downloadable datasets functions: hpaExport(), hpaSubset()

Examples

  histologyData <- hpaDownload(downloadList='histology', version='example')
  # tissueTranscriptData <- hpaDownload('RNA transcript tissue')

trannhatanh89/HPAanalyze documentation built on June 6, 2023, 4:31 p.m.