Case-insensitive substring search (SQL ILIKE) over SRA study titles
and abstracts, or GEO series titles and summaries. The successor to
SRAdb::getSRA() for finding studies; it is a plain pattern match,
not a ranked full-text search.
Arguments
- con
A connection from
omicidx_connect(), or anomicidx_db().- query
character(1). Text to find.
%matches any run of characters and_any single character, so"single cell%glioma"finds both phrases in that order.- limit
integer(1). Maximum number of rows to return.
Value
A tibble of matching studies (sra_search(): from
sradb.study) or series (geo_search(): from geometadb.gse).
In geo_search() results, type, bioprojects and
sra_studies
are list-columns, since a series can have several of each; use
tidyr::unnest_longer() to get one row per value.
Examples
con <- omicidx_connect()
sra_search(con, "single cell%glioma", limit = 5)
#> # A tibble: 5 × 7
#> study_accession study_title study_type study_abstract center_name
#> <chr> <chr> <chr> <chr> <chr>
#> 1 ERP144083 Longitudinal scRNA-Seq … Transcrip… Longitudinal … DKTK Clini…
#> 2 SRP042161 Single cell RNA-seq of … Transcrip… We report tra… GEO
#> 3 SRP060524 Single cell RNA-seq ana… Transcrip… To understand… GEO
#> 4 SRP067604 Single cell transcripto… Transcrip… Radiation is … GEO
#> 5 SRP081644 An automatec microwell … Other We report an … GEO
#> # ℹ 2 more variables: bioproject_accession <chr>, geo_accession <chr>
series <- geo_search(con, "glioblastoma", limit = 5)
if (requireNamespace("tidyr", quietly = TRUE)) {
tidyr::unnest_longer(series[c("gse", "sra_studies")], "sra_studies")
}
#> # A tibble: 2 × 2
#> gse sra_studies
#> <chr> <chr>
#> 1 GSE102136 SRP114556
#> 2 GSE108013 SRP126639
DBI::dbDisconnect(con)