Skip to contents

Search the Human Protein Atlas

Source: R/search.R
hpaSearch.Rd

Query the Human Protein Atlas search API directly from R, equivalent to searching at https://www.proteinatlas.org/search and downloading the resulting tsv file. See https://www.proteinatlas.org/about/help/dataaccess for the full query syntax and list of available column codes.

Usage

hpaSearch(search, columns = c("g", "gs", "eg"), exact = FALSE)

Arguments

A string with the search term(s) or query, using the same syntax as https://www.proteinatlas.org/search. This can be a simple term (e.g. 'TP53') or an advanced field query (e.g. 'protein_class:CD markers AND normal_expression:Cerebral cortex;Any;Not detected,Low').

columns

A vector or comma-separated string of column codes to retrieve, e.g. c('g', 'gs', 'eg') or 'g,gs,eg'. See https://www.proteinatlas.org/about/help/dataaccess for the full list of available codes. Defaults to gene name, gene synonym, and Ensembl id.

exact

Logical. The HPA search itself always matches on partial and related terms (e.g. searching 'TP53' also returns 'TP53BP1' and other related genes). If TRUE, the result is filtered down, after retrieval, to rows whose Gene column is an exact match for search. Requires 'g' (gene name) to be included in columns, since that's what the filtering is done on. Only meaningful when search is a single gene symbol, not an advanced field query.

Value

A tibble with one row per matching protein/gene and one column per requested field, using the HPA's own column names (e.g. Gene, Ensembl).

See also

hpaSubset hpaXmlGet

Examples

  hpaSearch(search = 'TP53', columns = c('g', 'gs', 'eg'))
#> # A tibble: 45 × 3
#>    Gene     `Gene synonym`                                               Ensembl
#>    <chr>    <chr>                                                        <chr>  
#>  1 TP53     LFS1, p53                                                    ENSG00…
#>  2 TP53INP1 DKFZp434M1317, FLJ22139, P53DINP1, SIP, Teap, TP53INP1A, TP… ENSG00…
#>  3 TP53TG3  P53TG3, TP53TG3A                                             ENSG00…
#>  4 TP53RK   BUD32, C20orf64, dJ101A2.2, Nori-2p, prpk, TPRKB             ENSG00…
#>  5 TP53TG3B NA                                                           ENSG00…
#>  6 TP53TG3C NA                                                           ENSG00…
#>  7 TP53TG3D NA                                                           ENSG00…
#>  8 TP53TG3E NA                                                           ENSG00…
#>  9 TP53TG3F NA                                                           ENSG00…
#> 10 TP53TG5  C20orf10, CLG01, dJ453C12.5                                  ENSG00…
#> # ℹ 35 more rows
  hpaSearch(search = 'TP53', columns = c('g', 'gs', 'eg'), exact = TRUE)
#> # A tibble: 1 × 3
#>   Gene  `Gene synonym` Ensembl        
#>   <chr> <chr>          <chr>          
#> 1 TP53  LFS1, p53      ENSG00000141510