## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() suppressPackageStartupMessages(library(grasp2db)) ## ----loadup2------------------------------------------------------------- library(grasp2db) ## ----grasp2-------------------------------------------------------------- grasp2 <- GRASP2() grasp2 ## ----lkp----------------------------------------------------------------- variant <- tbl(grasp2, "variant") q1 = (variant %>% select(Pvalue, NegativeLog10PBin) %>% filter(NegativeLog10PBin > 8) %>% summarize(maxp = max(Pvalue), n=n())) q1 ## ----lkex---------------------------------------------------------------- explain(q1) ## ----lkp2---------------------------------------------------------------- study <- tbl(grasp2, "study") large_effect <- variant %>% select(PMID, SNPid_dbSNP134, NegativeLog10PBin) %>% filter(NegativeLog10PBin > 5) phenotype <- left_join(large_effect, study %>% select(PMID, PaperPhenotypeDescription)) phenotype ## ----doasth-------------------------------------------------------------- lkaw <- semi_join( variant %>% filter(NegativeLog10PBin <= 4) %>% select(PMID, chr_hg19, SNPid_dbSNP134, PolyPhen2), study %>% filter(PaperPhenotypeDescription == "Asthma")) ## ----dogre--------------------------------------------------------------- lkaw %>% filter(PolyPhen2 %like% "%amaging%") ## ----lkbasic------------------------------------------------------------- grasp2 ## ----lkcon--------------------------------------------------------------- gcon = grasp2$con library(RSQLite) gcon dbListTables(gcon) ## ----getgw--------------------------------------------------------------- library(gwascat) data(gwrngs19) # hg19 addresses; NHGRI ships hg38 gwrngs19 ## ----lkanti-------------------------------------------------------------- gr22 = variant %>% filter(chr_hg19 == "22") abs22 = checkAnti("22") 1 - (abs22 %>% nrow()) / (gr22 %>% count %>% collect %>% `[[`("n")) ## ----lkabs--------------------------------------------------------------- abs22