extractByProbes {gQTLBase} | R Documentation |
retrieve eqtlTest results from a ciseStore instance
extractByProbes(store, probeids, extractTag = "probeid") extractByRanges(store, gr) extractBySymbols(store, symbols, sym2probe, extractTag = "probeid")
store |
instance of |
probeids, symbols |
vector character tokens |
gr |
instance of |
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 |
an index will be searched if created by the ciseStore constructor
a GRanges instance
VJ Carey <stvjc@channing.harvard.edu>
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 }