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Jump to navigationJump to search- 13:34, 28 October 2013 diff hist +345 N 830 - MaqIndex::CompareToIndex() Created page with "<source lang="cpp"> int MaqIndex::CompareToIndex(String & sequence, unsigned int offset, unsigned int index) { index = sortedPositions[index]; for (unsigned int i = 0; i <..."
- 13:33, 28 October 2013 diff hist +137 Biostatistics 830 - Code Snippets →Code Snippets
- 13:29, 28 October 2013 diff hist +2,285 N 830 - BasicMapper::main() Created page with "<source lang="cpp"> int main(int argc, char ** argv) { // Record start time for this run time_t start = time(NULL); // This function summarizes available options and proc..." current
- 13:28, 28 October 2013 diff hist +266 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
- 13:26, 28 October 2013 diff hist +54 Biostatistics 830: Main Page →Required Reading
- 12:45, 25 October 2013 diff hist +220 Abecasis Lab →Former Doctoral Students
- 14:48, 14 October 2013 diff hist +95 RAREMETAL Documentation →Useful Wiki Pages
- 05:11, 11 October 2013 diff hist +93 Biostatistics 830: Main Page →Class Worksheets
- 05:10, 11 October 2013 diff hist 0 N File:Question Sheet - Li et al (2008) Genome Research.pdf current
- 11:13, 3 October 2013 diff hist +53 N RAREMETAL-SOFTWARE Goncalo moved page RAREMETAL-SOFTWARE to Rare Variant Analysis and Meta-Analysis current
- 11:13, 3 October 2013 diff hist 0 m Rare Variant Analysis and Meta-Analysis Goncalo moved page RAREMETAL-SOFTWARE to Rare Variant Analysis and Meta-Analysis current
- 16:16, 2 October 2013 diff hist 0 830 - Haplotyper::ImputeGenotypes() (edge) current
- 16:15, 2 October 2013 diff hist 0 830 - Haplotyper::ImputeGenotypes() (internal) current
- 16:03, 2 October 2013 diff hist 0 830 - Haplotyper::SampleOneHaplotype() current
- 15:55, 2 October 2013 diff hist -1 830 - Haplotyper::SummarizeOptions() current
- 15:06, 2 October 2013 diff hist +574 830 - MINIMAC::main() current
- 14:57, 2 October 2013 diff hist +421 830 - MINIMAC::main()
- 14:52, 2 October 2013 diff hist -1 830 - MINIMAC::main()
- 14:52, 2 October 2013 diff hist +11,013 N 830 - MINIMAC::main() Created page with "</source lang="cpp"> int main(int argc, char ** argv) { time_t start = time(NULL); printf("MiniMac - Imputation into phased haplotypes\n" "(c) 2010-2011 Goncalo..."
- 14:51, 2 October 2013 diff hist +27 Biostatistics 830 - Code Snippets →Code Snippets
- 14:31, 2 October 2013 diff hist +15 Biostatistics 830 - Code Snippets →Code Snippets
- 14:31, 2 October 2013 diff hist +75 N 830 - Haplotyper::ScoreLeftConditional smart() Goncalo moved page 830 - Haplotyper::ScoreLeftConditional smart() to 830 - Haplotyper::ScoreLeftConditional() (smart, complicated): Consistency. current
- 14:31, 2 October 2013 diff hist 0 m 830 - Haplotyper::ScoreLeftConditional() (smart, complicated) Goncalo moved page 830 - Haplotyper::ScoreLeftConditional smart() to 830 - Haplotyper::ScoreLeftConditional() (smart, complicated): Consistency. current
- 14:29, 2 October 2013 diff hist +215 830 - Haplotyper::ImputeGenotypes() (internal)
- 14:28, 2 October 2013 diff hist +645 N 830 - Haplotyper::ImputeGenotypes() (internal) Created page with "void Haplotyper::ImputeGenotypes(float * matrix1, float * matrix2, int marker) { posterior[0][marker] = posterior[1][marker] = posterior[2][marker] = 0.0; for (int i..."
- 14:26, 2 October 2013 diff hist +673 N 830 - Haplotyper::ImputeGenotypes() (edge) Created page with "<source lang="cpp"> void Haplotyper::ImputeGenotypes(float * matrix, int marker) { posterior[0][marker] = posterior[1][marker] = posterior[2][marker] = 0.0; for (in..."
- 14:25, 2 October 2013 diff hist +100 Biostatistics 830 - Code Snippets →Code Snippets
- 14:19, 2 October 2013 diff hist -498 830 - Haplotyper::ImputeGenotypes() current
- 14:16, 2 October 2013 diff hist -1 830 - Haplotyper::SampleOneHaplotype()
- 14:15, 2 October 2013 diff hist +198 830 - Haplotyper::SampleOneHaplotype()
- 14:14, 2 October 2013 diff hist +316 N 830 - Haplotyper::SampleOneHaplotype() Created page with "<source lang="cpp"> float Haplotyper::SampleOneHaplotype(float * vector, double first, double & second, float & choice) { for (second = 0; second < states; second++) ..."
- 14:14, 2 October 2013 diff hist +44 Biostatistics 830 - Code Snippets →Code Snippets
- 14:13, 2 October 2013 diff hist +2 830 - Haplotyper::SummarizeOptions()
- 14:13, 2 October 2013 diff hist +1,150 N 830 - Haplotyper::SummarizeOptions() Created page with "<code lang="cpp"> float Haplotyper::SummarizeOptions(float * vector, float ** left, float ** right, float theta, int first, int second) { right[0][0] = (1. - theta) * (..."
- 14:12, 2 October 2013 diff hist +42 Biostatistics 830 - Code Snippets →Code Snippets
- 14:11, 2 October 2013 diff hist +30 830 - Haplotyper::SampleChromosomes() current
- 14:11, 2 October 2013 diff hist +1,350 N 830 - Haplotyper::SampleChromosomes() Created page with " void Haplotyper::SampleChromosomes(Random * rand) { RewindMemoryPool(); RetrieveMemoryBlock(markers - 1); int first = 0, second = 0; SampleHaplotypes(leftMat..."
- 14:10, 2 October 2013 diff hist +9 830 - Haplotyper::SampleHaplotypes() current
- 14:08, 2 October 2013 diff hist -589 830 - Haplotyper::SampleHaplotypes()
- 14:08, 2 October 2013 diff hist +43 Biostatistics 830 - Code Snippets →Code Snippets
- 14:06, 2 October 2013 diff hist +4 830 - Haplotyper::SampleHaplotypes()
- 14:05, 2 October 2013 diff hist +1,364 N 830 - Haplotyper::SampleHaplotypes() Created page with "<source lang="cpp"> void Haplotyper::SampleChromosomes(Random * rand) { RewindMemoryPool(); RetrieveMemoryBlock(markers - 1); int first = 0, second = 0; Sampl..."
- 14:05, 2 October 2013 diff hist +42 Biostatistics 830 - Code Snippets →Code Snippets
- 13:30, 2 October 2013 diff hist +1 830 - Haplotyper::ScoreLeftConditional() current
- 13:27, 2 October 2013 diff hist -376 830 - Haplotyper::ScoreLeftConditional()
- 13:26, 2 October 2013 diff hist +966 N 830 - Haplotyper::ScoreLeftConditional() (smart, complicated) Created page with "<source lang="cpp"> // This version of the ScoreLeftConditional() function deals with sites // where no genotypes are observed a little more efficiently. // void Haplotyper:..."
- 13:25, 2 October 2013 diff hist +52 Biostatistics 830 - Code Snippets →Code Snippets
- 02:03, 27 September 2013 diff hist -16 Abecasis Lab →Staff
- 01:30, 27 September 2013 diff hist 0 Abecasis Lab →Former Research Fellows
- 15:01, 25 September 2013 diff hist +1,257 N 830 - MarkovModel::CountErrorsAndRecombinants() Created page with "<source lang="cpp"> void MarkovModel::CountErrorsAndRecombinants(char * observed, char ** haplotypes, float ** freq) { float * swap; float * vector = new float [state..." current
- 14:57, 25 September 2013 diff hist +508 N 830 - MarkovModel::CountErrors() Created page with "<source lang="cpp"> double MarkovModel::CountErrors(float * vector, char ** haplotypes, int position, char observed, double e, double freq) { if (observed == 0) re..." current
- 14:54, 25 September 2013 diff hist +487 N 830 - MarkovModel::CountRecombinants() Created page with "<source lang="cpp"> double MarkovModel::CountRecombinants(float * from, float * to, double r) { if (r == 0) return 0.0; double sum = 0.0; for (int i = 0; i ..." current
- 14:53, 25 September 2013 diff hist +135 Biostatistics 830 - Code Snippets →Code Snippets
- 14:50, 25 September 2013 diff hist +1,345 N 830 - MarkovModel::Impute() Created page with "<source lang="cpp"> void MarkovModel::Impute(char * major, char * observed, float * probs, char ** haplotypes, float ** freqs, int position) { d..." current
- 14:45, 25 September 2013 diff hist +33 Biostatistics 830 - Code Snippets →Code Snippets
- 14:45, 25 September 2013 diff hist +974 N 830 - MarkovModel::WalkRight() Created page with "<source lang="cpp"> void MarkovModel::WalkRight(char * major, char * observed, char ** haplotypes, float ** freqs) { float * swap; float * vector = new float [states]..." current
- 14:43, 25 September 2013 diff hist +36 Biostatistics 830 - Code Snippets →Code Snippets
- 14:42, 25 September 2013 diff hist +637 N 830 - MarkovModel::WalkLeft() Created page with "<source lang="cpp"> void MarkovModel::WalkLeft(char * observed, char ** haplotypes, float ** freqs) { // Initialize likelihoods at first position for (int i = 0; i < ..."
- 14:41, 25 September 2013 diff hist +35 Biostatistics 830 - Code Snippets →Code Snippets
- 14:40, 25 September 2013 diff hist -36 830 - MarkovModel::Condition() current
- 14:40, 25 September 2013 diff hist +476 N 830 - MarkovModel::Condition() Created page with "<source lang="cpp"> void MarkovModel::Condition(float * vector, char ** haplotypes, int position, char observed, double e, double freq) { if ..."
- 14:40, 25 September 2013 diff hist +1 Biostatistics 830 - Code Snippets →Code Snippets
- 14:40, 25 September 2013 diff hist +35 Biostatistics 830 - Code Snippets →Code Snippets
- 14:39, 25 September 2013 diff hist -202 830 - MarkovModel::Transpose() current
- 14:37, 25 September 2013 diff hist +767 N 830 - MarkovModel::Transpose() Created page with "<source lang="cpp"> void MarkovModel::Transpose(float * from, float * to, double r) { if (r == 0) for (int i = 0; i < states; i++) to[i] = from[i]; els..."
- 14:36, 25 September 2013 diff hist +2 Biostatistics 830 - Code Snippets →Code Snippets
- 14:36, 25 September 2013 diff hist +34 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
- 14:33, 25 September 2013 diff hist +72 Biostatistics 830: Main Page →Scheduling
- 14:33, 25 September 2013 diff hist 0 N File:Question Sheet - Li et al (2010) Gen Epid.pdf current
- 14:32, 25 September 2013 diff hist +81 Biostatistics 830: Main Page →Class Worksheets
- 14:32, 25 September 2013 diff hist 0 N File:Question Sheet - Howie et al (2012) Nat Genet.pdf current
- 14:31, 25 September 2013 diff hist +174 Biostatistics 830: Main Page →Scheduling
- 14:29, 25 September 2013 diff hist 0 N File:Question Sheet - Browing and Browning (2012) Am J Hum Genet.pdf current
- 11:00, 25 September 2013 diff hist +208 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
- 11:00, 25 September 2013 diff hist +54 Biostatistics 830: Main Page →Required Reading
- 10:59, 25 September 2013 diff hist +82 Biostatistics 830 - Code Snippets →Li et al (2010) Genet Epidemiol
- 10:58, 25 September 2013 diff hist +1,613 Biostatistics 830: Main Page →Scheduling
- 15:56, 13 September 2013 diff hist -163 830 - Haplotyper::RandomSetup() current
- 15:07, 13 September 2013 diff hist +16 Biostatistics 830: Main Page →Required Reading
- 15:06, 13 September 2013 diff hist -1 830 - Haplotyper::ImputeGenotypes()
- 15:06, 13 September 2013 diff hist +1,221 N 830 - Haplotyper::ImputeGenotypes() Created page with "</source lang="cpp"> void Haplotyper::ImputeGenotypes() { RewindMemoryPool(); // Process the last position RetrieveMemoryBlock(markers - 1); ImputeGenotypes(le..."
- 15:04, 13 September 2013 diff hist +41 Biostatistics 830 - Code Snippets →Code Snippets
- 15:02, 13 September 2013 diff hist +31 830 - Haplotyper::ScoreLeftConditional()
- 15:01, 13 September 2013 diff hist +797 N 830 - Haplotyper::ScoreLeftConditional() Created page with "void Haplotyper::ScoreLeftConditional() { ResetMemoryPool(); GetMemoryBlock(0); SetupPrior(leftMatrices[0]); ConditionOnData(leftMatrices[0], 0, current_genoty..."
- 15:00, 13 September 2013 diff hist +46 Biostatistics 830 - Code Snippets →Code Snippets
- 14:58, 13 September 2013 diff hist 0 830 - Haplotyper::ConditionOnData() current
- 14:58, 13 September 2013 diff hist +666 N 830 - Haplotyper::ConditionOnData() Created page with "<source code="cpp"> void Haplotyper::ConditionOnData(float * matrix, int marker, char genotype) { // We treat missing genotypes as uninformative about the mosaic's //..."
- 14:56, 13 September 2013 diff hist 0 830 - Haplotyper::SetupPrior() current
- 14:56, 13 September 2013 diff hist +324 N 830 - Haplotyper::SetupPrior() Created page with "<source code="cpp"> void Haplotyper::SetupPrior(float * matrix) { float prior = 1.0 / (states * states); for (int i = 0; i < states; i++) { for (int j = ..."
- 14:55, 13 September 2013 diff hist +77 Biostatistics 830 - Code Snippets →Code Snippets
- 14:52, 13 September 2013 diff hist +1,947 N 830 - Haplotyper::Transpose() Created page with "<source lang="cpp"> void Haplotyper::Transpose(float * source, float * dest, float theta) { // *source and *dest store a vector with likelihood information for each pos..." current
- 14:48, 13 September 2013 diff hist +1 Biostatistics 830 - Code Snippets →Code Snippets
- 14:48, 13 September 2013 diff hist +34 Biostatistics 830 - Code Snippets →Code Snippets
- 14:47, 13 September 2013 diff hist +91 830 - Haplotyper::RandomSetup()
- 14:46, 13 September 2013 diff hist +1,837 N 830 - Haplotyper::RandomSetup() Created page with "<source lang="cpp"> void Haplotyper::RandomSetup(Random * rand) { // access two arrays... // genotypes[i][j] includes genotypes for each individual // i..."
- 14:42, 13 September 2013 diff hist +37 Biostatistics 830 - Code Snippets →Code Snippets
- 14:38, 13 September 2013 diff hist +263 N Biostatistics 830 - Code Snippets Created page with "== Li et al (2010) Genet Epidemiol == === Full Citation === Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotyp..."
- 14:37, 13 September 2013 diff hist +16 Biostatistics 830: Main Page →Required Reading
- 14:37, 13 September 2013 diff hist +22 Biostatistics 830: Main Page →Required Reading
- 10:50, 9 September 2013 diff hist -2 Abecasis Group Awards