source("/home/valdar/cvs/stable/hs/bagphenotype/startup.R") bag.startup() data<-read.delim("/groups/flint/ILLUMINA/PHENOTYPES/FN.txt") fit <-data.frame(SUBJECT.NAME = rep(NA, length(data$SUBJECT.NAME)), Phenotype = rep (NA, length(data$SUBJECT.NAME))) fit$SUBJECT.NAME <- data$SUBJECT.NAME fit$Phenotype <- resid(survreg(Surv(FN.Latency,!FN.LatencyCensored) ~ EndNormalBW, data = data, na.action =na.exclude, dist='weibull', scale=1)) write.table(fit, file = "FN.resid", sep = "\t", quote = F, row.names = F) source("/home/valdar/cvs/stable/hs/bagphenotype/startup.R") bag.startup() data<-read.delim("/groups/flint/ILLUMINA/PHENOTYPES/EPM.txt") fit <-data.frame(SUBJECT.NAME = rep(NA, length(data$SUBJECT.NAME)), Phenotype = rep (NA, length(data$SUBJECT.NAME))) fit$Phenotype <- resid(survreg(Surv(1+EPM.OpenArmLatency,!EPM.OpenArmLatencyCensored) ~ EndNormalBW, data = data, na.action =na.exclude, dist='weibull', scale=1)) fit$SUBJECT.NAME <- data$SUBJECT.NAME write.table(fit, file = "EPM.OpenArmLatency.resid", sep = "\t", quote = F, row.names = F) data<-read.delim("/groups/flint/ILLUMINA/PHENOTYPES/OFT.txt") fit <-data.frame(SUBJECT.NAME = rep(NA, length(data$SUBJECT.NAME)), Phenotype = rep (NA, length(data$SUBJECT.NAME))) fit$Phenotype <- resid(survreg(Surv(1+OFT.Latency,!OFT.Latency.Censored) ~ EndNormalBW, data = data, na.action =na.exclude, dist='weibull', scale=1)) fit$SUBJECT.NAME <- data$SUBJECT.NAME write.table(fit, file = "OFT.Latency.resid", sep = "\t", quote = F, row.names = F)