NASA-GRSD-HS/6. Define QTL.R at master · elijahedmondson/NASA-GRSD-HS · GitHub

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# Function to pull all files from a directory folder and determine QTL of a given LOD score

define.QTL(dir = "~/Desktop/R/QTL/WD/7.\ Cataract/Logistic\ 2.0/", threshold = 5.73)

define.QTL = function(dir = "/Users/elijah/Desktop/files/", threshold = 5.73) {

        files <- (Sys.glob(paste0(dir,"*.Rdata")))

        for(j in 1:length(files)){
                LODmat = matrix(0, nrow = 20, ncol = 5, dimnames = list(1:20, c("LOD", "peak", "1.5 min", "1.5 max", "interval range")))

                load(file = files[j])
                print(files[j])

                for(i in 1:19) {
                        top = max(-log10(qtl[[i]]$p.value))
                        if(top > threshold) {

                                max.LOD.peak = qtl[[i]]@ranges[which(-log10(qtl[[i]]$p.value) == top)]

                                LOD.drop.int = top - 1.5
                                max.LOD.position = qtl[[i]]@ranges[which(-log10(qtl[[i]]$p.value) > max(LOD.drop.int))]

                                print(paste(i, max.LOD.position@start[1], max(max.LOD.position@start), top))

                                LODmat[i,] = c(top, ((min(max.LOD.peak@start) + max(max.LOD.peak@start))/2),
                                               max.LOD.position@start[1], max(max.LOD.position@start),
                                               (max(max.LOD.position@start) - max.LOD.position@start[1]))
                        }
                }
                write.csv(LODmat, file = paste0(files[j], "QTL", ".csv"))
                rm(qtl)
        }
}


xdefine.QTL = function(dir = "~/Desktop/R/QTL/WD/7.\ Cataract/Logistic\ 2.0/", threshold = 5.05) {

        files <- (Sys.glob(paste0(dir,"*.Rdata")))

        for(j in 1:length(files)){
                LODmat = matrix(0, nrow = 20, ncol = 6, dimnames = list(1:20, c("chr", "LOD", "peak", "1.5 min", "1.5 max", "interval range")))

                load(file = files[j])
                print(files[j])

                for(i in 1:19) {
                        top = max(-log10(qtl[[i]]$p.value))
                        if(top > threshold & top < 5.73) {
                                LOD.drop.int = top
                                max.LOD.peak <- qtl[[i]]@ranges[which(-log10(qtl[[i]]$p.value) > LOD.drop.int)]
                                max.LOD.position <- qtl[[i]]@ranges[which(-log10(qtl[[i]]$p.value) > LOD.drop.int)]
                                print(paste(i, max.LOD.position@start[1], max(max.LOD.position@start), top))

                                LODmat[i,] = c(i, top, ((min(max.LOD.peak@start) + max(max.LOD.peak@start))/2),
                                               max.LOD.position@start[1], max(max.LOD.position@start),
                                               (max(max.LOD.position@start) - max.LOD.position@start[1]))
                        }
                }
                write.csv(LODmat, file = paste0(files[j], "QTL", ".csv"))
                rm(qtl)
        }
}