dot-searchAnywhereSRA: Fulltext search in SRA

In ss-lab-cancerunit/SpiderSeqR: A Tool for Integration of Big Bio Data

Description

Fulltext search in SRA

Usage

.searchAnywhereSRA(
  SRA_query,
  acc_levels = c("run", "experiment", "sample", "study"),
  SRA_library_strategy = NULL,
  SRA_other_library_strategy = c("OTHER", "NA", "NULL"),
  ...
)

Arguments

SRA_query	Query passed to fts MATCH operator (cannot be a vector)
acc_levels	Character vector denoting which accession levels will be searched. Choose from some/all of c("run", "experiment", "sample", "study")
SRA_library_strategy	Character vector denoting library_strategy/ies of choice (OPTIONAL)
SRA_other_library_strategy	A character vector indicating whether (and which) uncategorised library strategies are accepted (choose between one and all elements of c("OTHER", "NA", "NULL")); if not desired, set equal to FALSE. NOTE: only evaluated if library strategy is provided
...	Other options

Value

Data frame with results

Examples

## stat3
# .searchAnywhereSRA("stat3") 

## stat3 in human samples
# .searchAnywhereSRA("stat3 taxon_id: 9606") 

## stat3 chip-seq (including unclassified library strategies)
# .searchAnywhereSRA("stat3", library_strategy = "ChIP-Seq")
## stat3 chip-seq not including unclassified library strategies
# .searchAnywhereSRA("stat3", 
#    library_strategy = "ChIP-Seq", 
#    SRA_other_library_strategy = FALSE) 

## stat3 ignoring matches at study level
#.searchAnywhereSRA("stat3", acc_levels = c("run", "experiment", "sample")) 

ss-lab-cancerunit/SpiderSeqR documentation built on Nov. 2, 2020, 12:18 a.m.