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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,109 @@ | ||
| HS.RMA.chrom = function(perms, chr, pheno, pheno.col, probs, K, addcovar, | ||
| markers, snp.file, outdir = "~/Desktop/", | ||
| tx = "", sanger.dir = "~/Desktop/R/QTL/WD/HS.sanger.files/") | ||
| { | ||
| begin <- Sys.time() | ||
| file.prefix = paste0("Bootstrap.", tx, ".", pheno.col, "(Chr", chr, ")") | ||
| plot.title = paste("Bootstrap ", tx, " ", pheno.col, " ", "(Chr ", chr, "):", sep = "") | ||
| print(paste(plot.title, Sys.time())) | ||
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| load(file = paste0(sanger.dir, "probs", chr, ".Rdata")) | ||
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| samples = intersect(rownames(pheno), rownames(probs)) | ||
| samples = intersect(samples, rownames(addcovar)) | ||
| samples = intersect(samples, rownames(K[[1]])) | ||
| stopifnot(length(samples) > 0) | ||
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| pheno = pheno[samples,,drop = FALSE] | ||
| addcovar = addcovar[samples,,drop = FALSE] | ||
| probs = probs[samples,,,drop = FALSE] | ||
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| #samples2 = markers$SNP_ID[which(markers$Chr == chr & markers$Mb_NCBI38 > (peakMB - 4000000) & markers$Mb_NCBI38 < (peakMB + 4000000))] | ||
| samples2 = markers$SNP_ID[which(markers$Chr == chr)] | ||
| probs = probs[,,samples2, drop = FALSE] | ||
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| K = K[[chr]][samples,samples,drop = FALSE] | ||
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| setwd(outdir) | ||
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| ## | ||
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| permutations = matrix(1, nrow = perms, ncol = 5, dimnames = list(1:perms, c("LOD", "min", "max", "average", "#Markers"))) | ||
| sanger.dir = sanger.dir | ||
| rm(samples, samples2) | ||
| for(p in 1:perms) { | ||
| LODtime = Sys.time() | ||
| print(p) | ||
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| #repeat { | ||
| phenoperm = data.frame(pheno[sample(nrow(pheno), replace = TRUE), ], | ||
| check.names = FALSE, check.rows = FALSE) | ||
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| samples = sub("\\.[0-9]$", "", rownames(phenoperm)) | ||
| probsperm = probs[samples,,] | ||
| rownames(probsperm) = make.unique(rownames(probsperm)) | ||
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| Kperm = K | ||
| Kperm = K[samples,samples,drop = FALSE] | ||
| rownames(Kperm) = make.unique(rownames(Kperm)) | ||
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| ### Move the model into the loop LOGISTIC REGRESSION MODEL ### | ||
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| Kperm = Kperm[samples, samples] | ||
| chrs = chr | ||
| data = vector("list", length(chrs)) | ||
| names(data) = chrs | ||
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| rng = which(markers[,2] == chrs) | ||
| data = list(probsperm = probsperm, Kperm = Kperm, | ||
| markers = markers[rng,]) | ||
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| result = vector("list", length(data)) | ||
| names(result) = names(data) | ||
| rm(probsperm, Kperm) | ||
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| ### WORK HORSE ### | ||
| ### RETURN ANY POS FOR ENRIRE CHROMOSOME ### | ||
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| result = GRSDbinom.permsfast(data, pheno = phenoperm, pheno.col, addcovar, tx, sanger.dir) | ||
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| top = max(-log10(result$pv)) | ||
| MAX.LOD = result$POS[which(-log10(result$pv) == top)] | ||
| MegaBase = (min(MAX.LOD) + max(MAX.LOD))/2000000 | ||
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| print(paste(MegaBase, "Mb: LOD", round(top, digits = 2))) | ||
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| #if (MAX.LOD > (peakMB - (window/2)) & MAX.LOD < (peakMB + (window/2))) break | ||
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| #} | ||
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| print(paste0("Accepted locus: ", MegaBase, " Mb")) | ||
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| # Save the locus. | ||
| permutations[p,] = c(top, min(MAX.LOD), max(MAX.LOD), ((min(MAX.LOD) + max(MAX.LOD))/2), length(MAX.LOD)) | ||
| print(paste(round(difftime(Sys.time(), LODtime, units = 'mins'), digits = 2), | ||
| "minutes...")) | ||
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| } | ||
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| print(paste(round(difftime(Sys.time(), begin, units = 'hours'), digits = 2), | ||
| "hours elapsed during analysis")) | ||
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| quant = quantile(permutations[,4], c(0.025,0.975)) | ||
| print(paste("95% Confidence Interval for QTL:", min(quant), "-", max(quant))) | ||
| print(paste("Interval =", (round((((max(quant) - min(quant))/1000000)), digits = 2)), "Mb")) | ||
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| return(permutations) | ||
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| }#HS.RMA.chrom() |
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