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explodecomputer / tryx

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Allow sig function to run if no associations for one of the categories #3

Open explodecomputer opened 6 years ago

explodecomputer commented 6 years ago

This happens e.g. if exposure is not from MR-Base and candidate->exposure traits can't be found in tryx.scan

e.g.

ua <- subset(gwas_catalog, grepl("Kottgen", Author) 
             & SNP %in% c('rs1471633', 'rs11264341', 'rs1260326', 'rs17050272', 'rs2307394', 'rs6770152', 'rs12498742', 
                          'rs2231142', 'rs17632159', 'rs675209', 'rs1165151', 'rs729761', 'rs1178977', 'rs10480300',
                          'rs17786744', 'rs2941484', 'rs1171614', 'rs10821905', 'rs2078267', 'rs478607', 'rs642803',
                          'rs3741414', 'rs653178', 'rs1394125', 'rs6598541', 'rs7193778', 'rs7188445', 'rs7224610', 
                          'rs2079742', 'rs164009')
             & Year == 2012
             & (Phenotype == 'Urate levels (mg/dl decrease)' | Phenotype == 'Urate levels (mg/dl increase)' | Phenotype == 'Urate levels (unit increase)'))

sample.size <- data.frame(SNP = c('rs1471633', 'rs11264341', 'rs1260326', 'rs17050272', 'rs2307394', 'rs6770152', 'rs12498742', 
                                  'rs2231142', 'rs17632159', 'rs675209', 'rs1165151', 'rs729761', 'rs1178977', 'rs10480300',
                                  'rs17786744', 'rs2941484', 'rs1171614', 'rs10821905', 'rs2078267', 'rs478607', 'rs642803',
                                  'rs3741414', 'rs653178', 'rs1394125', 'rs6598541', 'rs7193778', 'rs7188445', 'rs7224610', 
                                  'rs2079742', 'rs164009'),
                          samplesize = rep(110000, 30))
ua <- merge(ua, sample.size, by="SNP")
ua$Phenotype <- rep('Urate levels')
ua$units <- rep('mg/dl')
ua<-format_data(ua)

#Outcome
ao <- available_outcomes()
ao[grepl("Urate", ao$trait),]
gfr <-  extract_outcome_data(snps=ua$SNP, outcomes = 1105)

#Harmonization
dat <- harmonise_data(ua,gfr)

tryxscan <- tryx.scan(dat)
tryxscan <- tryx.sig(tryxscan)