gQTLBase (version 1.4.2)

extractByProbes: retrieve eqtlTest results from a ciseStore instance

Description

retrieve eqtlTest results from a ciseStore instance

Usage

extractByProbes(store, probeids, extractTag = "probeid")
extractByRanges(store, gr)
extractBySymbols(store, symbols, sym2probe, extractTag = "probeid")

Arguments

store

instance of ciseStore-class

probeids, symbols

vector character tokens

gr

instance of GRanges-class

sym2probe

named character vector of probeids with names given by corresponding symbols

extractTag

character atom telling what field in the archived GRanges is regarded as the probe or gene identifier

...

extra arguments to extractByProbes

Value

• a GRanges instance

Details

an index will be searched if created by the ciseStore constructor

Examples

if (require(geuvStore2)) {
 store = makeGeuvStore2()
 ebp = extractByProbes(store, c("ENSG00000183814.10", "ENSG00000174827.9"))
 ebp
 rr = range(ebp)
 ebr = extractByRanges(store, rr)
 ebr
 s2p = structure(c("ENSG00000183814.10", "ENSG00000163207.5", "ENSG00000228449.1", 
	"ENSG00000137962.8", "ENSG00000232848.1", "ENSG00000227280.1", 
	"ENSG00000238081.1", "ENSG00000117480.10", "ENSG00000253368.2", 
	"ENSG00000174827.9"), .Names = c("LIN9", "IVL", "RP11-177A2.4", 
	"ARHGAP29", "CTA-215D11.4", "RP11-458D21.2", "RP4-620F22.3", 
	"FAAH", "TRNP1", "PDZK1"))
 ss = extractBySymbols(store, c("IVL", "FAAH", "PDZK1"), s2p)
 ss
 }