ROH-sliding-window-based run detection

進入文件數據文件夾和激活conda

cd /
cd /mnt/d/peng/goat/sixregions
conda activate seletion
R
library(detectRUNS)

進行ROH檢測

genotypeFilePath <- ("/mnt/d/peng/goat/sixregions/Africa.ped")
mapFilePath <- ("/mnt/d/peng/goat/sixregions/Africa.map")
slidingRuns <- slidingRUNS.run(
genotypeFile = genotypeFilePath,
mapFile = mapFilePath,
windowSize = 50, threshold = 0.05,
minSNP = 20, ROHet = FALSE,
maxOppWindow = 1,
maxMissWindow = 1,
maxGap = 10^6,
minLengthBps = 200000,
minDensity = 1/10^5)

4. 生成統計列表

summaryList <- summaryRuns( runs = slidingRuns, mapFile = mapFilePath, genotypeFile = genotypeFilePath, Class = 4, snpInRuns = TRUE)
str (summaryList)

5輸出結果

write.csv (summaryList $summary_ROH_count_chr, file ="/mnt/d/peng/goat/sixregions/summary_ROH_count_chr.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE) write.csv (summaryList$ summary_ROH_percentage_chr, file ="/mnt/d/peng/goat/sixregions/summary_ROH_percentage_chr.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE)
write.csv (summaryList $summary_ROH_count , file ="/mnt/d/peng/goat/sixregions/summary_ROH_count .csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE) write.csv (summaryList$ summary_ROH_percentage , file ="/mnt/d/peng/goat/sixregions/summary_ROH_percentage .csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE)
write.csv (summaryList $summary_ROH_mean_chr , file ="/mnt/d/peng/goat/sixregions/summary_ROH_mean_chr.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE) write.csv (summaryList$ summary_ROH_mean_class, file ="/mnt/d/peng/goat/sixregions/summary_ROH_mean_class.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE)
write.csv (summaryList $result_Froh_genome_wide, file ="/mnt/d/peng/goat/sixregions/result_Froh_genome_wide.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE) write.csv (summaryList$ result_Froh_chromosome_wide, file ="/mnt/d/peng/goat/sixregions/result_Froh_chromosome_wide.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE)
write.csv (summaryList $result_Froh_class, file ="/mnt/d/peng/goat/sixregions/result_Froh_class.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE) write.csv (summaryList$ SNPinRun , file ="/mnt/d/peng/goat/sixregions/SNPinRun-20.csv", sep =" ", row.names =TRUE, col.names =TRUE, quote =TRUE)