# # # R代码从装饰图案的CSAR来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:设置# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 60)选项(继续= " ")选项(提示=“R >”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:loadData # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(CSAR)数据(“CSAR-dataset”);头(sampleSEP3_test)头(controlSEP3_test) nhitsS < -mappedReads2Nhits (sampleSEP3_test、文件=“sampleSEP3_test”= c (CHR1v01212004”),从而向chrL = c (10000)) nhitsC < -mappedReads2Nhits (controlSEP3_test、文件=“controlSEP3_test”= c (“CHR1v01212004”),从而向chrL = c (10000)) nhitsC文件名nhitsS文件名美元# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:runScore # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #测试< -ChIPseqScore(控制= nhitsC示例= nhitsS文件=“测试”,倍= 10000)测试文件名美元赢得< -sigWin(测试)头(赢得)score2wig(测试、文件=“test.wig”倍= 10000)d < -distance2Genes(赢=赢,人造石铺地面= TAIR8_genes_test) d基因< -genesWithPeaks (d)头(基因)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:runPermutation # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # permutatedWinScores (nn = 1,样品= sampleSEP3_test控制= controlSEP3_test fileOutput =“测试”,= c (“CHR1v01212004”),从而向chrL = c (100000)) permutatedWinScores (nn = 2,样品= sampleSEP3_test控制= controlSEP3_test fileOutput =“测试”,= c (“CHR1v01212004”),从而向chrL = c (100000)) nulldist < -getPermutatedWinScores(文件=“测试”,nn = 1:2) getThreshold (winscores =值(赢得)得分,美元permutatedScores = nulldist,罗斯福= . 05)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:CSAR。Rnw: 97 - 98 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # sessionInfo ()