Incorporated Danny's code for calculating QTL main effects into rqtl_wrapper.R

1 files changed, 43 insertions, 0 deletions

diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R
index 20c0e06..523888f 100644
--- a/scripts/rqtl_wrapper.R
+++ b/scripts/rqtl_wrapper.R
@@ -269,4 +269,47 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){
   verbose_print('Running scanone\n')
   qtl_results = scanone(cross_object, pheno.col=1, model=opt$model, method=opt$method)
 }
+
+#QTL main effects on adjusted longevity
+getEffects <- function(sdata, gtsprob, marker = "1_24042124", model = "longevity ~ sex + site + cohort + treatment", trait = "longevity"){
+  rownames(sdata) <- 1:nrow(sdata)
+  rownames(gtsprob) <- 1:nrow(gtsprob)
+  mp <- gtsprob[, grep(marker, colnames(gtsprob))]
+  gts <- unlist(lapply(lapply(lapply(apply(mp,1,function(x){which(x > 0.85)}),names), strsplit, ":"), function(x){
+    if(length(x) > 0){ return(x[[1]][2]); }else{ return(NA) }
+  }))
+
+  ismissing <- which(apply(sdata, 1, function(x){any(is.na(x))}))
+  if(length(ismissing) > 0){
+    sdata <- sdata[-ismissing, ]
+    gts <- gts[-ismissing]
+  }
+
+  mlm <- lm(as.formula(model), data = sdata)
+  pheAdj <- rep(NA, nrow(sdata))
+  adj <- residuals(mlm) + mean(sdata[, trait])
+  pheAdj[as.numeric(names(adj))] <- adj
+  means <- c(mean(pheAdj[which(gts == "AC")],na.rm=TRUE),mean(pheAdj[which(gts == "AD")],na.rm=TRUE),mean(pheAdj[which(gts == "BC")],na.rm=TRUE),mean(pheAdj[which(gts == "BD")],na.rm=TRUE))
+  std <- function(x) sd(x,na.rm=TRUE)/sqrt(length(x))
+  stderrs <- c(std(pheAdj[which(gts == "AC")]),std(pheAdj[which(gts == "AD")]),std(pheAdj[which(gts == "BC")]),std(pheAdj[which(gts == "BD")]))
+  paste0(round(means,0), " ± ", round(stderrs,2))
+}
+
+if (type == "4-way") {
+  verbose_print("Get phenotype name + genoprob + all phenotypes + models for 4-way crosses")
+  traitname <- colnames(pull.pheno(cross_object))[1]
+  gtsp <- pull.genoprob(cross_object)
+  allpheno <- pull.pheno(cross_object)
+  model <- paste0(traitname, " ~ ", paste0(covar_names, sep="", collapse=" + "))
+
+  meffects <- c()
+  verbose_print("Getting QTL main effects for 4-way crosses")
+  for(marker in  rownames(qtl_results)){
+    meff <- getEffects(allpheno, gtsp, marker = marker, model, trait = traitname)
+    meffects <- rbind(meffects, meff)
+  }
+  qtl_results <- cbind(data.frame(qtl_results[,1:3]), meffects)
+  colnames(qtl_results)[4:7] <- c("AC", "AD", "BC", "BD")
+}
+
 write.csv(qtl_results, out_file)