| Previous changeset 28:896eb8ae1c8c (2022-10-27) Next changeset 30:8ff2c287ff1c (2022-10-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 83864e12abbf63728a389b7fe677f3b88844e03f |
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modified:
mqppep_anova_script.Rmd |
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| diff -r 896eb8ae1c8c -r 42b207aaa527 mqppep_anova_script.Rmd --- a/mqppep_anova_script.Rmd Thu Oct 27 19:48:51 2022 +0000 +++ b/mqppep_anova_script.Rmd Thu Oct 27 22:11:38 2022 +0000 |
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| b'@@ -106,171 +106,7 @@\n # to the directory where they should be writtn\n debugFileBasePath: !r if (TRUE) NULL else "test-data"\n ---\n-<!--\n- alphaFile: "test-data/alpha_levels.tabular"\n- inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"\n- preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"\n- kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]\n- regexSampleNames: "\\\\.\\\\w+\\\\.\\\\d+[A-Z]$"\n- regexSampleGrouping: "\\\\w+"\n- groupFilterPatterns: ".+"\n- groupFilter: !r c("none", "exclude", "include")[3]\n- imputationMethod: !r c("group-median", "median", "mean", "random")[1]\n- kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[1]\n- ut_alphaFile: "test-data/alpha_levels.tabular"\n- ut_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"\n- ut_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"\n- ut_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]\n- ut_regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- ut_regexSampleGrouping: "\\\\d+"\n- ut_groupFilterPatterns: ".+,.*"\n- ut_groupFilter: !r c("none", "exclude", "include")[1]\n- ut_imputationMethod: !r c("group-median", "median", "mean", "random")[4]\n- ut_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]\n- tst_alphaFile: "test-data/alpha_levels.tabular"\n- tst_inputFile: "test-data/test_input_for_anova.tabular"\n- tst_preprocDb: "test-data/test_input_for_anova.sqlite"\n- tst_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]\n- tst_regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- tst_regexSampleGrouping: "\\\\d+"\n- tst_groupFilterPatterns: ".+"\n- tst_groupFilter: !r c("none", "exclude", "include")[1]\n- tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4]\n- tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5]\n-\n- tst_alphaFile: "test-data/alpha_levels.tabular"\n- tst_inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"\n- tst_preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"\n- tst_kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]\n- tst_regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- tst_regexSampleGrouping: "\\\\d+"\n- tst_groupFilterPatterns: ".+,.*"\n- tst_groupFilter: !r c("none", "exclude", "include")[1]\n- tst_imputationMethod: !r c("group-median", "median", "mean", "random")[4]\n- tst_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]\n- px_alphaFile: "test-data/alpha_levels.tabular"\n- px_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"\n- px_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"\n- px_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]\n- px_regexSampleNames: "\\\\.\\\\w+\\\\.\\\\d+[A-Z]$"\n- px_regexSampleGrouping: "\\\\w+"\n- px_groupFilterPatterns: ".+"\n- px_groupFilter: !r c("none", "exclude", "include")[3]\n- px_imputationMethod: !r c("group-median", "median", "mean", "random")[4]\n- px_kseaCutoffThreshold: !r c(0.05, 0.1, 0.20, 0.35, 0.4, 0.5, 0.999)[5]\n- pdx_alphaFile: "test-data/alpha_levels.tabular"\n- pdx_inputFile: "test-data/PDX012970_pST.preproc_tab.tabular"\n- pdx_preprocDb: "test-data/PDX012970_pST.preproc.sqlite"\n- pdx_kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2]\n- pdx_regexSampleNames: "\\\\.\\\\w+\\\\.\\\\w+\\\\.\\\\d+[A-Z]$"\n- pdx_regexSampleGrouping: "\\\\.\\\\w+\\\\K\\\\.\\\\w+"\n- pdx_groupFilterPatterns: "AdCa,AVPC"\n- pdx_groupFilter: !r c("none", "exclude", "include")[3]\n- pdx_imputationMethod: !r c("group-median", "median", "mean", "random")[4]\n- pdx_kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[1]\n- tst_alphaFile: '..b'st-data/pST_Sites_NancyDu.txt.preproc.tabular"\n- nd_preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"\n- nd_kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]\n- nd_regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- nd_regexSampleGrouping: "\\\\d+"\n- nd_groupFilterPatterns: ".+,.*"\n- nd_groupFilter: !r c("none", "exclude", "include")[1]\n- nd_imputationMethod: !r c("group-median", "median", "mean", "random")[4]\n- pxd_alphaFile: "test-data/alpha_levels.tabular"\n- pxd_inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"\n- pxd_preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"\n- pxd_kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]\n- pxd_regexSampleNames: "\\\\.\\\\w+\\\\.\\\\d+[A-Z]$"\n- pxd_regexSampleGrouping: "\\\\w+"\n- pxd_groupFilterPatterns: ".+"\n- pxd_groupFilter: !r c("none", "exclude", "include")[3]\n- pxd_imputationMethod: !r c("group-median", "median", "mean", "random")[4]\n-\n- alphaFile: "test-data/alpha_levels.tabular"\n- inputFile: "test-data/test_input_for_anova.tabular"\n- preprocDb: "test-data/test_input_for_anova.sqlite"\n- kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]\n- regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- regexSampleGrouping: "\\\\d+"\n- groupFilterPatterns: ".+,.*"\n- groupFilter: !r c("none", "exclude", "include")[1]\n-\n- alphaFile: "test-data/alpha_levels.tabular"\n- inputFile: "test-data/PDX012970_pST.preproc_tab.tabular"\n- preprocDb: "test-data/PDX012970_pST.preproc.sqlite"\n- kseaAppPrepDb: !r c(":memory:", "test-data/PDX012970.sqlite")[2]\n- regexSampleNames: "\\\\.\\\\w+\\\\.\\\\w+\\\\.\\\\d+[A-Z]$"\n- regexSampleGrouping: "\\\\.\\\\w+\\\\K\\\\.\\\\w+"\n- groupFilterPatterns: "AdCa,AVPC"\n- groupFilter: !r c("none", "exclude", "include")[3]\n-\n- alphaFile: "test-data/alpha_levels.tabular"\n- inputFile: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_tab.tabular"\n- preprocDb: "test-data/PDX_pST_by_trt.ppep_intensities.ppep_map.preproc_sqlite.sqlite"\n- kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2]\n- regexSampleNames: "\\\\.\\\\w+\\\\.\\\\d+[A-Z]$"\n- regexSampleGrouping: "\\\\w+"\n- groupFilterPatterns: ".+,.*"\n- groupFilter: !r c("none", "exclude", "include")[3]\n-\n- kseaCutoffStatistic: !r c("p.value", "FDR")[2]\n- kseaCutoffThreshold: !r c(0.05, 0.1)[1]\n-\n- alphaFile: "test-data/alpha_levels.tabular"\n- inputFile: "test-data/UT_phospho_ST_sites.preproc.tabular"\n- preprocDb: "test-data/UT_phospho_ST_sites.preproc.sqlite"\n- kseaAppPrepDb: !r c(":memory:", "test-data/UT_phospho_ST_sites.ksea.sqlite")[2]\n- regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- regexSampleGrouping: "\\\\d+"\n-\n- alphaFile: "test-data/alpha_levels.tabular"\n- inputFile: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.tabular"\n- preprocDb: "test-data/pY_Sites_NancyDu.txt.ppep_intensities.ppep_map.preproc.sqlite"\n- kseaAppPrepDb: !r c(":memory:", "test-data/pY_Sites_NancyDu.ksea.sqlite")[2]\n- regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- regexSampleGrouping: "\\\\d+"\n- groupFilterPatterns: ".+,.*"\n- groupFilter: !r c("none", "exclude", "include")[3]\n-\n- alphaFile: "test-data/alpha_levels.tabular"\n- inputFile: "test-data/pST_Sites_NancyDu.txt.preproc.tabular"\n- preprocDb: "test-data/pST_Sites_NancyDu.txt.preproc.sqlite"\n- kseaAppPrepDb: !r c(":memory:", "test-data/pST_Sites_NancyDu.ksea.sqlite")[2]\n- regexSampleNames: "\\\\.\\\\d+[A-Z]$"\n- regexSampleGrouping: "\\\\d+"\n- groupFilterPatterns: ".+,.*"\n- groupFilter: !r c("none", "exclude", "include")[1]\n-\n--->\n+\n ```{r setup, include = FALSE, results = \'asis\'}\n \n # simple debug messaging\n' |