Browse code

Added preprocessCore_*_stubs.h

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/preprocessCore@54042 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 25/03/2011 14:42:31
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 Package: preprocessCore
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-Version: 1.13.5
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+Version: 1.13.6
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 Title: A collection of pre-processing functions
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 Author: Benjamin Milo Bolstad <bmb@bmbolstad.com>
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 Maintainer: Benjamin Milo Bolstad <bmb@bmbolstad.com>
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@@ -10,4 +10,3 @@ License: LGPL (>= 2)
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 Collate:  normalize.quantiles.R quantile_extensions.R rma.background.correct.R rcModel.R colSummarize.R subColSummarize.R plmr.R plmd.R
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 LazyLoad: yes
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 biocViews: Infrastructure
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+void rma_bg_parameters(double *PM,double *param, int rows, int cols, int column);
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+void rma_bg_adjust(double *PM,double *param, int rows, int cols, int column);
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+void rma_bg_correct(double *PM, int rows, int cols);
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+int qnorm_c(double *data, int *rows, int *cols);
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+int qnorm_robust_c(double *data,double *weights, int *rows, int *cols, int *use_median, int *use_log2, int *weight_scheme);
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+int qnorm_c_using_target(double *data, int *rows, int *cols, double *target, int *targetrows);
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+int qnorm_c_determine_target(double *data, int *rows, int *cols, double *target, int *targetrows);
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+int qnorm_c_within_blocks(double *x, int *rows, int *cols, int *blocks);
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+void averagelog_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
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+void averagelog(double *data, int rows, int cols, double *results, double *resultsSE);
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+void AverageLog(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void AverageLog_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
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+void logaverage(double *data, int rows, int cols, double *results, double *resultsSE);
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+void LogAverage(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void LogAverage_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
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+void tukeybiweight(double *data, int rows, int cols, double *results, double *resultsSE);
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+void tukeybiweight_no_log(double *data, int rows, int cols, double *results, double *resultsSE);
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+void TukeyBiweight(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void TukeyBiweight_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
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+void TukeyBiweight_no_log_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
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+void lm_wfit(double *x, double *y, double *w, int rows, int cols, double tol, double *out_beta, double *out_resids);
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+void median_polish_fit_no_copy(double *data, int rows, int cols, double *r, double *c, double *t);
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+void median_polish_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
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+void median_polish_log2_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
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+void median_polish_log2(double *data, int rows, int cols, double *results, double *resultsSE, double *residuals);
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+void median_polish(double *data, int rows, int cols, double *results, double *resultsSE, double *residuals);
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+void MedianPolish(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void MedianPolish_no_log(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void rlm_fit(double *x, double *y, int rows, int cols, double *out_beta, double *out_resids, double *out_weights, double (* PsiFn)(double, double, int), double psi_k, int max_iter,int initialized);
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+void rlm_wfit(double *x, double *y, double *w, int rows, int cols, double *out_beta, double *out_resids, double *out_weights, double (* PsiFn)(double, double, int), double psi_k, int max_iter,int initialized);
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+void rlm_fit_anova(double *y, int y_rows, int y_cols,double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void rlm_wfit_anova(double *y, int y_rows, int y_cols, double *w, double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void rlm_compute_se(double *X,double *Y, int n, int p, double *beta, double *resids,double *weights,double *se_estimates,double *varcov, double *residSE, int method,double (* PsiFn)(double, double, int), double psi_k);
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+void rlm_compute_se_anova(double *Y, int y_rows,int y_cols, double *beta, double *resids,double *weights,double *se_estimates, double *varcov, double *residSE, int method,double (* PsiFn)(double, double, int), double psi_k);
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+void MedianLog(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void MedianLog_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
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+void medianlog(double *data, int rows, int cols, double *results, double *resultsSE);
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+void medianlog_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
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+void LogMedian(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void LogMedian_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void logmedian(double *data, int rows, int cols, double *results, double *resultsSE);
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+void logmedian_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
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+void colaverage_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
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+void colaverage(double *data, int rows, int cols, double *results, double *resultsSE);
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+void ColAverage(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void ColAverage_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
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+void colmedian_no_copy(double *data, int rows, int cols, double *results, double *resultsSE);
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+void colmedian(double *data, int rows, int cols, double *results, double *resultsSE);
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+void ColMedian(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes, double *resultsSE);
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+void ColMedian_noSE(double *data, int rows, int cols, int *cur_rows, double *results, int nprobes);
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+void plmr_fit(double *y, int y_rows, int y_cols,double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void plmr_wfit(double *y, int y_rows, int y_cols, double *w, double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void plmrr_fit(double *y, int y_rows, int y_cols,double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void plmrc_fit(double *y, int y_rows, int y_cols,double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void plmrr_wfit(double *y, int y_rows, int y_cols, double *w, double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void plmrc_wfit(double *y, int y_rows, int y_cols, double *w, double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double, double, int), double psi_k,int max_iter, int initialized);
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+void rlm_fit_anova_given_probe_effects(double *y, int y_rows, int y_cols, double *probe_effects, double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double,double, int), double psi_k,int max_iter, int initialized);
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+void rlm_compute_se_anova_given_probe_effects(double *Y, int y_rows,int y_cols, double *probe_effects,double *beta, double *resids,double *weights,double *se_estimates, double *varcov, double *residSE, int method,double (* PsiFn)(double, double, int), double psi_k);
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+void rlm_wfit_anova_given_probe_effects(double *y, int y_rows, int y_cols, double *probe_effects, double *w, double *out_beta, double *out_resids, double *out_weights,double (* PsiFn)(double,double, int), double psi_k,int max_iter, int initialized);