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Merge pull request #13 from yfyang86/v0.0.2
V0.0.2
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| ./simulation | ||
| simulation/* | ||
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| .vscode | ||
| .vscode | ||
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| .so | ||
| .o | ||
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| proc2 | ||
| .proc2 | ||
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| src/vstack.o\ | ||
| src/segmentstack.o\ | ||
| src/mtc.o\ | ||
| src/utils.o\ | ||
| src/metseg.o | ||
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| #!/usr/local/bin/Rscript | ||
| args = commandArgs(trailingOnly=TRUE) | ||
| data <- read.table(args[1], header = T) | ||
| ## users could change the p-value adjustment method | ||
| if (length(args) == 1){ | ||
| method = "fdr" | ||
| }else{ | ||
| if (args[2] %in% c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")){ | ||
| method = args[2] | ||
| }else{ | ||
| method = "fdr" | ||
| } | ||
| } | ||
| data$FDR <- p.adjust(data$pFN, method = method) | ||
| names(data)[ncol(data)] = toupper(method) | ||
| write.table(data, file = paste("test.mr.DMR.", method, sep = '') , | ||
| row.names= F, sep = "\t", quote = F) |
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| #include <fstream> | ||
| #include <string> | ||
| #include <iomanip> | ||
| #include <sstream> | ||
| #include <iostream> | ||
| #include <map> | ||
| #include <random> | ||
| #include "utils.h" | ||
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| bool inx_tie_incr(inx_tie x, inx_tie y){ | ||
| return (x.value < y.value); | ||
| } | ||
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| bool inx_tie_decr(inx_tie x, inx_tie y){ | ||
| return (y.value < x.value); | ||
| } | ||
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| static std::map<std::string, int> solver_sam_load_config_setting(){ | ||
| /* | ||
| a: 0.67672 | ||
| b: -0.03785 | ||
| c: 0. | ||
| d: 0. | ||
| */ | ||
| std::map<std::string, int> s_config; | ||
| s_config["a"] = 0; | ||
| s_config["b"] = 1; | ||
| s_config["c"] = 2; | ||
| s_config["d"] = 3; | ||
| s_config["useBartlett"]=4; | ||
| s_config["useFoldedNormal"]=5; | ||
| return s_config; | ||
| } | ||
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| void solver_sam_load_config(double * config){ | ||
| std::string line; | ||
| std::ifstream config_file("config.txt"); | ||
| std::string option; | ||
| double option_val; | ||
| static std::map<std::string, int> s_congfig = solver_sam_load_config_setting(); | ||
| std::map<std::string, int>::iterator it; | ||
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| for (size_t j=0; j<4; j++) config[j] = 0.; | ||
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| if (!config_file.is_open()) { | ||
| std::cerr << "Could not open the file - '" | ||
| << "config.txt" << "'" << std::endl; | ||
| exit(EXIT_FAILURE); | ||
| }else { | ||
| while ( getline (config_file,option, ':') && getline (config_file,line) ){ | ||
| std::istringstream(line) >> option_val; | ||
| it = s_congfig.find(option); | ||
| if (it!=s_congfig.end()) config[it->second] = option_val; | ||
| } | ||
| config_file.close(); | ||
| } | ||
| } | ||
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| /** BH method Randomize break the tie | ||
| * @brief | ||
| * By applying the above formulation, the FDR controlling MCP introduced in | ||
| * Benjamini and Hochberg (1995) can be rephrased into a FDR $p$-value | ||
| * adjustment. Benjamini and Hochberg's MCP is as follows: compare each | ||
| * ordered $p$-value $p_{(i)}$ with $\alpha \cdot i / m$. | ||
| * Let $k=\max \left\{i: p_{(i)} \leqslant \alpha \cdot i / m\right\}$, | ||
| * if such $k$ exists reject $\mathrm{H}_{(1)}^0, \ldots, \mathrm{H}_{(k)}^0$. | ||
| * A $q$ sized $\mathrm{MCP}$ rejects an hypotheses $\mathrm{H}_{(i)}^0$ | ||
| * if for some $k, k=i, \ldots, m, p_{(k)} \cdot m / k \leqslant \alpha$, | ||
| * thus we define the BH FDR $p$-value adjustment as | ||
| * $$ | ||
| * Q_{\text {adj }}^{\mathrm{BH}}\left(p_{(i)}\right) | ||
| * = | ||
| * \min _{i \leqslant k}\left\{p_{(k)} \cdot m / k\right\} | ||
| * $$ | ||
| * @example{ | ||
| * std::vector<double> ex; | ||
| * for (auto v : padj_bh(ex)){ | ||
| * std::cout<<v<<"\t"; | ||
| * } | ||
| * } | ||
| */ | ||
| std::vector<double> padj_bh(std::vector<double> & x){ | ||
| /* | ||
| i <- lp:1L | ||
| o <- order(p, decreasing = TRUE) | ||
| ro <- order(o) | ||
| pmin(1, cummin(n/i * p[o]))[ro] | ||
| */ | ||
| order_tie tmp_tie; | ||
| int cnt = 1; | ||
| std::map<int, order_tie> xp; | ||
| std::vector<inx_tie> yinx; | ||
| std::vector<inx_tie> roinx; | ||
| inx_tie xxxx; | ||
| int m = ((int) x.size()); | ||
| std::vector<int> xorder; | ||
| std::vector<int> xorderinc; | ||
| std::vector<double> y = x; | ||
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| for (auto xui:x){ | ||
| xxxx.inx = cnt - 1; | ||
| xxxx.value = xui; | ||
| yinx.push_back(xxxx); | ||
| cnt++; | ||
| } | ||
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| std::sort(yinx.begin(), yinx.end(), inx_tie_decr);//decreasing | ||
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| cnt = 1; | ||
| for (auto xui:yinx){ | ||
| xxxx.inx = cnt - 1; | ||
| xxxx.value = (double) xui.inx; | ||
| roinx.push_back(xxxx); | ||
| cnt++; | ||
| } | ||
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| std::sort(roinx.begin(), roinx.end(), inx_tie_incr);//increasing | ||
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| for (int i = 0; i< m; ++i){// n log(n) | ||
| xorder.push_back(i); | ||
| xorderinc.push_back(i); | ||
| } | ||
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| for (int i = 0; i< m; ++i){ | ||
| xorder[i] = yinx[i].inx; // n | ||
| xorderinc[i] = roinx[i].inx; | ||
| } | ||
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| for (int i = 0; i< m; ++i){ | ||
| x[i] = yinx[i].value * m /(m-i+.0); | ||
| } | ||
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| for (int i = 0; i< m; ++i){ | ||
| if (i+1 < m && x[i+1]>x[i]){ | ||
| x[i+1] = x[i]; | ||
| } | ||
| } | ||
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| for (int i = 0; i< m; ++i){ | ||
| y[i] = x[xorderinc[i]]; | ||
| y[i] = ( | ||
| (y[i] > 1. || (!std::isfinite(y[i]))? 1. : y[i]) | ||
| ); | ||
| } | ||
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| return y; | ||
| } | ||
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| @@ -0,0 +1,35 @@ | ||
| #ifndef MAIN_UTILS_H | ||
| #define MAIN_UTILS_H | ||
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| #include <fstream> | ||
| #include <string> | ||
| #include <iomanip> | ||
| #include <sstream> | ||
| #include <iostream> | ||
| #include <map> | ||
| #include <random> | ||
| #include <map> | ||
| #include <algorithm> | ||
| #include <vector> | ||
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| static std::map<std::string, int> solver_sam_load_config_setting(); | ||
| void solver_sam_load_config(double * conifg); | ||
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| struct order_tie | ||
| { | ||
| double value; | ||
| std::vector<int> loc; | ||
| int cnt; | ||
| }; | ||
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| struct inx_tie{ | ||
| double value; | ||
| int inx; | ||
| }; | ||
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| bool inx_tie_incr(inx_tie x, inx_tie y); | ||
| bool inx_tie_decr(inx_tie x, inx_tie y); | ||
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| std::vector<double> padj_bh(std::vector<double> & x); | ||
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| #endif |
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