searchForTerm: Search for samples matching criteria of interest
In ss-lab-cancerunit/SpiderSeqR: A Tool for Integration of Big Bio Data

Description Usage Arguments Value Argument requirements Further information Examples

searchForTerm provides an automated framework for searching within SRA database for samples matching a range of different criteria (e.g. experimental method, tissue type). It also supplements the sample information with data from GEO (if available)

searchForTerm(
  SRA_library_strategy,
  gene = NULL,
  antibody = NULL,
  cell_type = NULL,
  treatment = NULL,
  species = NULL,
  platform = NULL,
  SRA_secondary_library_strategy = NULL,
  return_all = TRUE
)

`SRA_library_strategy`	Experimental method (e.g. RNA-Seq, ChIP-Seq). Only one SRA_library_strategy is allowed in a single query. To get a list of available library strategies, run `getDatabaseInformation()`
`gene`	A character vector with genes of interest (it is recommended to provide a few synonyms)
`antibody`	A character vector with antibodies of interest (it is recommended to provide a few synonyms, please note that some studies annotate their antibodies with trade names/symbols)
`cell_type`	A character vector describing source types of interest (cell type, tissue, organ etc.)
`treatment`	A character vector with keywords regarding treatment protocol
`species`	A character vector with taxonomy IDs (e.g. "9606" for human)
`platform`	A character vector with sequencing platforms
`SRA_secondary_library_strategy`	Additional experimental method of interest filtered from the studies featured in search results
`return_all`	A logical indicating what results should be returned. FALSE means that only samples matching criteria of interest will be returned (and their putative inputs/controls for RNA-Seq or ChIP-Seq). TRUE means that the whole SRPs will be returned(containing matching samples, but also all the other samples within an SRP). Defaults to TRUE

Nothing. Creates a range of files with the query information and search results.

REQUIRED: SRA_library_strategy AND at least one of: gene, antibody, cell_type or treatment

OPTIONAL: species, platform, SRA_secondary_library_strategy

For further information (especially on the output files) please refer to the package vignettes.

startSpiderSeqRDemo()
#Simple search
searchForTerm(SRA_library_strategy = "ChIP-Seq", gene = "sir3")
#searchForTerm(SRA_library_strategy = "RNA-Seq", 
#    gene = c("p53", "tp53"), species = "9606") 

#Search with parameters stored in a list
#st <- list(SRA_library_strategy="ChIP-Seq", gene="STAT1", antibody="STAT1")
#do.call(searchForTerm, st)