# # # R代码从装饰图案来源的小插曲/触发/本月/ doc /触发。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:进口# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(触发)数据(酵母)的名字(酵母)#减少数据大小的小插图运行时set.seed(123) # 400年的特征子集选择gidx =排序(样本(1:6216、大小= 400))$ exp =酵母酵母exp (gidx,)酵母exp美元。pos =酵母exp美元。标记的pos (gidx] #选择子集midx =排序(样本(1:3244、大小= 500))酵母酵母标志=美元标志midx,酵母美元标志。pos =酵母$标记。pos (midx,)附加(酵母)暗(exp) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:构建# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #三角。obj < -触发器。构建(=标记,标记实验= exp marker.pos =标记。pos exp.pos = exp.pos)三角。obj分离(酵母)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:链接# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #三角。obj = trigger.link(三角。obj,规范= TRUE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:图一# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #(三角。obj类型=“链接”,截止= 1 e-5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:触发器。Rnw: 163 - 164 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #(三角。obj类型=“链接”,截止= 1 e-5) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:mlink # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #三角。obj = trigger.loclink (trig.obj)三角。obj = trigger.mlink(三角。obj, B = 10, idx = NULL) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:图# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #地块(三角。obj类型=“mlink”, qcut = 0.2,本。大小= 50000)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:触发器。Rnw: 191 - 192 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #(三角。obj类型=“mlink”, qcut = 0.2,本。size = 50000) ################################################### ### code chunk number 9: eigenR2 ################################################### trig.obj = trigger.eigenR2(trig.obj, adjust = FALSE) ################################################### ### code chunk number 10: fig3 ################################################### plot(trig.obj, type = "eigenR2") ################################################### ### code chunk number 11: trigger.Rnw:212-213 ################################################### plot(trig.obj, type = "eigenR2") ################################################### ### code chunk number 12: trigger.net ################################################### trig.obj = trigger.loclink(trig.obj, window.size = 10000) trig.prob = trigger.net(trig.obj, Bsec = 100, idx = NULL) dim(trig.prob) ################################################### ### code chunk number 13: detach ################################################### # Re-attach dataset to re-include all traits for analysis data(yeast); attach(yeast) dim(exp) trig.obj <- trigger.build(marker=marker, exp=exp, marker.pos=marker.pos, exp.pos=exp.pos) ################################################### ### code chunk number 14: export2cross ################################################### cross = trigger.export2cross(trig.obj, plotarg = FALSE, verbose = FALSE) ################################################### ### code chunk number 15: trait-trigger ################################################### causreg = trigger.trait(trig.obj, trait = "DSE1", cross = cross, addplot = TRUE, thr = 3) causreg