diff options
| -rw-r--r-- | scripts/rqtl_wrapper.R | 95 |
1 files changed, 49 insertions, 46 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index 5ecd774..ea2c345 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -178,6 +178,9 @@ if (!is.null(opt$pairscan)) { } else if (!is.null(opt$interval)) { verbose_print('Calculating genotype probabilities with interval mapping\n') cross_object <- calc.genoprob(cross_object, step=5, stepwidth="max") +} else if (!is.null(opt$pairscan)) { + verbose_print('Calculating genotype probabilities for pair-scan\n') + cross_object <- calc.genoprob(cross_object, step=10) } else { verbose_print('Calculating genotype probabilities\n') cross_object <- calc.genoprob(cross_object) @@ -294,57 +297,57 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){ qtl_results = scan_func(cross_object, pheno.col=1, model=opt$model, method=opt$method) } -#QTL main effects on adjusted longevity -getEffects <- function(sdata, gtsprob, marker = "1_24042124", model = "longevity ~ sex + site + cohort + treatment", trait = "longevity"){ - rownames(sdata) <- 1:nrow(sdata) - rownames(gtsprob) <- 1:nrow(gtsprob) - mp <- gtsprob[, grep(marker, colnames(gtsprob))] - gts <- unlist(lapply(lapply(lapply(apply(mp,1,function(x){which(x > 0.85)}),names), strsplit, ":"), function(x){ - if(length(x) > 0){ return(x[[1]][2]); }else{ return(NA) } - })) - - ismissing <- which(apply(sdata, 1, function(x){any(is.na(x))})) - if(length(ismissing) > 0){ - sdata <- sdata[-ismissing, ] - gts <- gts[-ismissing] - } - - mlm <- lm(as.formula(model), data = sdata) - pheAdj <- rep(NA, nrow(sdata)) - adj <- residuals(mlm) + mean(sdata[, trait]) - pheAdj[as.numeric(names(adj))] <- adj - means <- c(mean(pheAdj[which(gts == "AC")],na.rm=TRUE),mean(pheAdj[which(gts == "AD")],na.rm=TRUE),mean(pheAdj[which(gts == "BC")],na.rm=TRUE),mean(pheAdj[which(gts == "BD")],na.rm=TRUE)) - std <- function(x) sd(x,na.rm=TRUE)/sqrt(length(x)) - stderrs <- c(std(pheAdj[which(gts == "AC")]),std(pheAdj[which(gts == "AD")]),std(pheAdj[which(gts == "BC")]),std(pheAdj[which(gts == "BD")])) - paste0(round(means,0), " ± ", round(stderrs,2)) -} - -if (type == "4-way") { - verbose_print("Get phenotype name + genoprob + all phenotypes + models for 4-way crosses") - traitname <- colnames(pull.pheno(cross_object))[1] - gtsp <- pull.genoprob(cross_object) - allpheno <- pull.pheno(cross_object) - if (!is.null(opt$addcovar)) { - model <- paste0(traitname, " ~ ", paste0(covar_names, sep="", collapse=" + ")) - } else { - model <- paste0(traitname, " ~ 1 ") - } - - 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") -} - verbose_print('Writing results to CSV file\n') if (!is.null(opt$pairscan)) { map_out_file = file.path(opt$outdir, paste("MAP_", opt$filename, sep = "" )) write.csv(qtl_results[1], out_file) write.csv(qtl_results[2], map_out_file) } else { + # QTL main effects on adjusted longevity + getEffects <- function(sdata, gtsprob, marker = "1_24042124", model = "longevity ~ sex + site + cohort + treatment", trait = "longevity"){ + rownames(sdata) <- 1:nrow(sdata) + rownames(gtsprob) <- 1:nrow(gtsprob) + mp <- gtsprob[, grep(marker, colnames(gtsprob))] + gts <- unlist(lapply(lapply(lapply(apply(mp,1,function(x){which(x > 0.85)}),names), strsplit, ":"), function(x){ + if(length(x) > 0){ return(x[[1]][2]); }else{ return(NA) } + })) + + ismissing <- which(apply(sdata, 1, function(x){any(is.na(x))})) + if(length(ismissing) > 0){ + sdata <- sdata[-ismissing, ] + gts <- gts[-ismissing] + } + + mlm <- lm(as.formula(model), data = sdata) + pheAdj <- rep(NA, nrow(sdata)) + adj <- residuals(mlm) + mean(sdata[, trait]) + pheAdj[as.numeric(names(adj))] <- adj + means <- c(mean(pheAdj[which(gts == "AC")],na.rm=TRUE),mean(pheAdj[which(gts == "AD")],na.rm=TRUE),mean(pheAdj[which(gts == "BC")],na.rm=TRUE),mean(pheAdj[which(gts == "BD")],na.rm=TRUE)) + std <- function(x) sd(x,na.rm=TRUE)/sqrt(length(x)) + stderrs <- c(std(pheAdj[which(gts == "AC")]),std(pheAdj[which(gts == "AD")]),std(pheAdj[which(gts == "BC")]),std(pheAdj[which(gts == "BD")])) + paste0(round(means,0), " ± ", round(stderrs,2)) + } + + if (type == "4-way") { + verbose_print("Get phenotype name + genoprob + all phenotypes + models for 4-way crosses") + traitname <- colnames(pull.pheno(cross_object))[1] + gtsp <- pull.genoprob(cross_object) + allpheno <- pull.pheno(cross_object) + if (!is.null(opt$addcovar)) { + model <- paste0(traitname, " ~ ", paste0(covar_names, sep="", collapse=" + ")) + } else { + model <- paste0(traitname, " ~ 1 ") + } + + 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) } |