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Convert between SRA, GEO, BioSample and BioProject accessions

Source: R/sradb.R
sra_convert.Rd

The successor to SRAdb::sraConvert() and GEOmetadb::geoConvert(). Accessions of any supported type, mixed freely, are mapped to the requested types.

Usage

sra_convert(con, in_acc, out_type = c("study", "sample", "experiment", "run"))

geo_convert(con, in_acc, out_type = c("gse", "gpl", "gsm"))

Arguments

con

A connection from omicidx_connect(), or an omicidx_db().

in_acc

character. Accessions to convert; in_list in GEOmetadb::geoConvert().

out_type

character. Accession types to return.

Value

A tibble with one column per input type present and per out_type, with one row per distinct combination. NA where an accession has no link of that type.

Details

Supported types: SRA study (SRP/ERP/DRP), sample (SRS/ERS/DRS), experiment (SRX/ERX/DRX) and run (SRR/ERR/DRR); biosample (SAMN/SAMEA/SAMD); bioproject (PRJNA/PRJEB/PRJDB); and GEO gse, gsm and gpl. SRA accessions are linked through runs (sradb.sra), so experiments without runs are not found, and GEO samples link to SRA through their SRA experiment. Converting a GPL returns every sample on that platform, which can be large.

Examples

con <- omicidx_connect()
sra_convert(con, "SRP000001")
#> # A tibble: 83 × 4
#>    study     sample    experiment run      
#>    <chr>     <chr>     <chr>      <chr>    
#>  1 SRP000001 SRS000100 SRX000007  SRR000001
#>  2 SRP000001 SRS000100 SRX000006  SRR000008
#>  3 SRP000001 SRS000100 SRX000003  SRR000020
#>  4 SRP000001 SRS000100 SRX000005  SRR000025
#>  5 SRP000001 SRS000605 SRX000001  SRR000026
#>  6 SRP000001 SRS000100 SRX000004  SRR000032
#>  7 SRP000001 SRS000605 SRX000001  SRR000035
#>  8 SRP000001 SRS000100 SRX000003  SRR000038
#>  9 SRP000001 SRS000605 SRX000001  SRR000045
#> 10 SRP000001 SRS000605 SRX000002  SRR000055
#> # ℹ 73 more rows
geo_convert(con, "GSE164073", c("gsm", "run"))
#> # A tibble: 72 × 3
#>    run         gse       gsm       
#>    <chr>       <chr>     <chr>     
#>  1 SRR13332243 GSE164073 GSM4996084
#>  2 SRR13332250 GSE164073 GSM4996086
#>  3 SRR13332252 GSE164073 GSM4996086
#>  4 SRR13332260 GSE164073 GSM4996088
#>  5 SRR13332266 GSE164073 GSM4996090
#>  6 SRR13332267 GSE164073 GSM4996090
#>  7 SRR13332271 GSE164073 GSM4996091
#>  8 SRR13332278 GSE164073 GSM4996093
#>  9 SRR13332283 GSE164073 GSM4996094
#> 10 SRR13332287 GSE164073 GSM4996095
#> # ℹ 62 more rows
DBI::dbDisconnect(con)