######################## ### B_625_625 ######################## library(compcodeR) hoge <- generateSyntheticData(dataset = "B_625_625", n.vars = 12500, samples.per.cond = 5, n.diffexp = 1250, repl.id = 1, seqdepth = 1e7, fraction.upregulated = 0.5, between.group.diffdisp = FALSE, filter.threshold.total = 1, filter.threshold.mediancpm = 0, fraction.non.overdispersed = 0, output.file = "hoge.rds") runDiffExp(data.file = "hoge.rds", result.extent = "voom.limma", Rmdfunction = "voom.limma.createRmd", output.directory = ".", norm.method = "TMM") runDiffExp(data.file = "hoge.rds", result.extent = "edgeR.exact", Rmdfunction = "edgeR.exact.createRmd", output.directory = ".", norm.method = "TMM", trend.method = "movingave", disp.type = "tagwise") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq.nbinom", Rmdfunction = "DESeq.nbinom.createRmd", output.directory = ".", sharing.mode = "maximum", disp.method = "pooled", fit.type = "parametric") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq2", Rmdfunction = "DESeq2.createRmd", output.directory = ".", fit.type = "parametric", test = "wald") runDiffExp(data.file = "hoge.rds", result.extent = "SAMseq", Rmdfunction = "SAMseq.createRmd", output.directory = ".") runDiffExp(data.file = "hoge.rds", result.extent = "TCC", Rmdfunction = "TCC.createRmd", output.directory = ".", norm.method = "tmm", test.method="edger") runComparisonGUI(input.directories = ".", output.directory = ".", recursive = FALSE) ######################## ### B_1250_0 ######################## library(compcodeR) hoge <- generateSyntheticData(dataset = "B_1250_0", n.vars = 12500, samples.per.cond = 5, n.diffexp = 1250, repl.id = 1, seqdepth = 1e7, fraction.upregulated = 1.0, between.group.diffdisp = FALSE, filter.threshold.total = 1, filter.threshold.mediancpm = 0, fraction.non.overdispersed = 0, output.file = "hoge.rds") runDiffExp(data.file = "hoge.rds", result.extent = "voom.limma", Rmdfunction = "voom.limma.createRmd", output.directory = ".", norm.method = "TMM") runDiffExp(data.file = "hoge.rds", result.extent = "edgeR.exact", Rmdfunction = "edgeR.exact.createRmd", output.directory = ".", norm.method = "TMM", trend.method = "movingave", disp.type = "tagwise") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq.nbinom", Rmdfunction = "DESeq.nbinom.createRmd", output.directory = ".", sharing.mode = "maximum", disp.method = "pooled", fit.type = "parametric") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq2", Rmdfunction = "DESeq2.createRmd", output.directory = ".", fit.type = "parametric", test = "wald") runDiffExp(data.file = "hoge.rds", result.extent = "SAMseq", Rmdfunction = "SAMseq.createRmd", output.directory = ".") runDiffExp(data.file = "hoge.rds", result.extent = "TCC", Rmdfunction = "TCC.createRmd", output.directory = ".", norm.method = "tmm", test.method="edger") runComparisonGUI(input.directories = ".", output.directory = ".", recursive = FALSE) ######################## ### B_2000_2000 ######################## library(compcodeR) hoge <- generateSyntheticData(dataset = "B_2000_2000", n.vars = 12500, samples.per.cond = 5, n.diffexp = 4000, repl.id = 1, seqdepth = 1e7, fraction.upregulated = 0.5, between.group.diffdisp = FALSE, filter.threshold.total = 1, filter.threshold.mediancpm = 0, fraction.non.overdispersed = 0, output.file = "hoge.rds") runDiffExp(data.file = "hoge.rds", result.extent = "voom.limma", Rmdfunction = "voom.limma.createRmd", output.directory = ".", norm.method = "TMM") runDiffExp(data.file = "hoge.rds", result.extent = "edgeR.exact", Rmdfunction = "edgeR.exact.createRmd", output.directory = ".", norm.method = "TMM", trend.method = "movingave", disp.type = "tagwise") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq.nbinom", Rmdfunction = "DESeq.nbinom.createRmd", output.directory = ".", sharing.mode = "maximum", disp.method = "pooled", fit.type = "parametric") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq2", Rmdfunction = "DESeq2.createRmd", output.directory = ".", fit.type = "parametric", test = "wald") runDiffExp(data.file = "hoge.rds", result.extent = "SAMseq", Rmdfunction = "SAMseq.createRmd", output.directory = ".") runDiffExp(data.file = "hoge.rds", result.extent = "TCC", Rmdfunction = "TCC.createRmd", output.directory = ".", norm.method = "tmm", test.method="edger") runComparisonGUI(input.directories = ".", output.directory = ".", recursive = FALSE) ######################## ### B_4000_0 ######################## library(compcodeR) hoge <- generateSyntheticData(dataset = "B_4000_0", n.vars = 12500, samples.per.cond = 5, n.diffexp = 4000, repl.id = 1, seqdepth = 1e7, fraction.upregulated = 1.0, between.group.diffdisp = FALSE, filter.threshold.total = 1, filter.threshold.mediancpm = 0, fraction.non.overdispersed = 0, output.file = "hoge.rds") runDiffExp(data.file = "hoge.rds", result.extent = "voom.limma", Rmdfunction = "voom.limma.createRmd", output.directory = ".", norm.method = "TMM") runDiffExp(data.file = "hoge.rds", result.extent = "edgeR.exact", Rmdfunction = "edgeR.exact.createRmd", output.directory = ".", norm.method = "TMM", trend.method = "movingave", disp.type = "tagwise") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq.nbinom", Rmdfunction = "DESeq.nbinom.createRmd", output.directory = ".", sharing.mode = "maximum", disp.method = "pooled", fit.type = "parametric") runDiffExp(data.file = "hoge.rds", result.extent = "DESeq2", Rmdfunction = "DESeq2.createRmd", output.directory = ".", fit.type = "parametric", test = "wald") runDiffExp(data.file = "hoge.rds", result.extent = "SAMseq", Rmdfunction = "SAMseq.createRmd", output.directory = ".") runDiffExp(data.file = "hoge.rds", result.extent = "TCC", Rmdfunction = "TCC.createRmd", output.directory = ".", norm.method = "tmm", test.method="edger") runComparisonGUI(input.directories = ".", output.directory = ".", recursive = FALSE)