hpaSubset {HPAanalyze} | R Documentation

## Subset downloaded data

### Description

`hpaSubset()` subsets data by gene name, tissue, cell type, cancer and/or cell line. The input is the list object generated by `hpaDownload()` or as the output of another `hpaSubset()`. Use `hpaListParam()` to see the list of available parameters for a specific list object. Will not work on isoform data.

`hpaListParam()` list available variables in downloaded data that can be used as parameters to subset the data via `hpaSubset()`. This function work with the data object generated by `hpaDownload()` or a previous call of `hpaSubset()`.

### Usage

    hpaSubset(data = NULL, targetGene = NULL, targetTissue = NULL,
      targetCellType = NULL, targetCancer = NULL, targetCellLine = NULL)

    hpaListParam(data = NULL)

### Arguments

`data` | Input the list object generated by `hpaDownload()` or `hpaSubset()`
`targetGene` | Vector of strings of HGNC gene symbols. It will be used to subset every dataset in the list object. You can also mix HGNC gene symbols and ensemnl ids (start with ENSG) and they will be converted to HGNC gene symbols.
`targetTissue` | Vector of strings of normal tissues. Will be used to subset the `normal_tissue` and `rna_tissue` dataset.
`targetCellType` | Vector of strings of normal cell types. Will be used to subset the `normal_tissue` dataset.
`targetCancer` | Vector of strings of cancer types. Will be used to subset the `pathology` dataset.
`targetCellLine` | Vector of strings of cell lines. Will be used to subset the `rna_cell_line` dataset.

### Value

`hpaSubset` will return a list of tibbles as the result of subsetting, depending on the input data.

The output of `hpaListParam()` is a list of vectors containing all subset parameter for the downloaded data.

### See Also

Other downloadable datasets functions: `hpaDownload`, `hpaExport`

### Examples

      downloadedData <- hpaDownload(downloadList='all', version='example')
      geneList <- c('TP53', 'EGFR')
      tissueList <- c('breast', 'cerebellum', 'skin 1')
      cancerList <- c('breast cancer', 'glioma', 'melanoma')

      subsetData <- hpaSubset(data=downloadedData,
                              targetGene=geneList,
                              targetTissue=tissueList,
                              targetCancer=cancerList)

      downloadedData <- hpaDownload(downloadList='all', version='example')
      params <- hpaListParam(data=downloadedData)
      params$normal_tissue

[Package HPAanalyze version 1.2.1 Index]