# # # R代码从装饰图案的polyfit来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:polyfit。Rnw: 40-41 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(Polyfit) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:Polyfit。Rnw: 84 - 91 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # cd < - makeExampleCountDataSet () cd < - estimateSizeFactors (cds) cd < - estimateDispersions (cds)电视台< - nbinomTest (cd,“A”、“B”) pValuesDESeq < -电视台美元pval # <——原始DESeq代码nbTPolyfit < - pfNbinomTest (cd,“A”、“B”) pValuesPFDESeq < - nbTPolyfit $ pval # <——Polyfit替换# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:fig2plot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # oldpar < - par (mfrow = c(1、2)嘘(pValuesDESeq休息= seq (0 1 = 0.01), xlab =“假定值”,主要=“DESeq”)嘘(pValuesPFDESeq休息= seq (0 1 = 0.01), xlab =“假定值”,主要=“polyfit-DESeq”)票面(oldpar) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:图# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # oldpar < - par (mfrow = c(1、2)嘘(pValuesDESeq休息= seq (0 1 = 0.01), xlab =“假定值”,主要=“DESeq”)嘘(pValuesPFDESeq休息= seq (0 1 = 0.01), xlab =“假定值”,主要=“polyfit-DESeq”)票面(oldpar) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:Polyfit。Rnw: 160 - 166 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # lP < - levelPValues (pValuesPFDESeq) outTable <——cbind (origPval = pValuesPFDESeq levelledPval = lP pValueCorr美元,levelledQval = lP qValueCorr美元,BH_Qval = lP qValueCorrBH美元)头(outTable) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:fig5plot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # lP <——levelPValues (pValuesPFDESeq、情节= TRUE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:图# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # lP < - levelPValues (pValuesPFDESeq、情节= TRUE)