# # # R代码从装饰图案的GlobalAncovaDecomp来源。rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:GlobalAncovaDecomp。rnw: 25-32 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(Biobase)库(GlobalAncova)数据(vantVeer)数据(phenodata)数据(途径)如果<——sessionInfo()选项(宽度= 70)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 2号代码块:数据# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(GlobalAncova)数据(vantVeer)数据(phenodata)数据(途径)公式< - - - - - - ~ +转移+年级ERstatus # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:连续的# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # GlobalAncova.decomp (xx = vantVeer =公式,公式模型。dat = phenodata方法=“顺序”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:GlobalAncovaDecomp。rnw: 111 - 113 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # formula2 < - ~ ERstatus +转移+年级GlobalAncova.decomp (xx = vantVeer公式= formula2模型。dat = phenodata方法=“顺序”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:type3 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # GlobalAncova.decomp (xx = vantVeer =公式,公式模型。dat = phenodata方法= " type3”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:pathw # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # GlobalAncova.decomp (xx = vantVeer =公式,公式模型。dat = phenodata =“type3”方法,测试。基因=通路[1:3])# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:genewise # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # GlobalAncova.decomp (xx = vantVeer公式=公式,模型。dat = phenodata测试。基因=通路[[1]][1:3],genewise = TRUE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:plotseq (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #阴谋。顺序(vantVeer公式= ~ ERstatus +转移+等级,模型。dat = phenodata测试。基因=通路[[3]],名字。geneset =“细胞周期通路”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:GlobalAncovaDecomp。rnw: 191 - 192 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #阴谋。顺序(vantVeer公式= ~ ERstatus +转移+等级,模型。dat = phenodata测试。genes = pathways[[3]], name.geneset = "cell cycle pathway") ################################################### ### code chunk number 10: combplot (eval = FALSE) ################################################### ## Plot.all(vantVeer, formula = ~ ERstatus + metastases + grade, model.dat = phenodata, test.genes = pathways[[3]], name.geneset = "cell cycle pathway") ################################################### ### code chunk number 11: GlobalAncovaDecomp.rnw:213-214 ################################################### Plot.all(vantVeer, formula = ~ ERstatus + metastases + grade, model.dat = phenodata, test.genes = pathways[[3]], name.geneset = "cell cycle pathway") ################################################### ### code chunk number 12: pairwise ################################################### pair.compare(xx = vantVeer, formula = ~ grade, model.dat = phenodata, group = "grade", perm = 100) ################################################### ### code chunk number 13: GlobalAncovaDecomp.rnw:271-272 ################################################### data(colon.tumour) ################################################### ### code chunk number 14: groene ################################################### data(colon.tumour) data(colon.normal) data(colon.pheno) formula <- ~ UICC.stage + sex + location GlobalAncova.decomp(xx = colon.tumour, formula = formula, model.dat = colon.pheno, method = "type3") ################################################### ### code chunk number 15: diff ################################################### GlobalAncova.decomp(xx = colon.tumour - colon.normal, formula = formula, model.dat = colon.pheno, method = "type3") ################################################### ### code chunk number 16: zz ################################################### GlobalAncova.decomp(xx = colon.tumour, formula = formula, model.dat = colon.pheno, method = "all", zz = colon.normal) ################################################### ### code chunk number 17: zzgw ################################################### GlobalAncova.decomp(xx = colon.tumour, formula = formula, model.dat = colon.pheno, method = "all", zz = colon.normal, zz.per.gene = TRUE)