User contributions for Goncalo

25 September 2013

• 14:5714:57, 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
• 14:5414:54, 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
• 14:5314:53, 25 September 2013 diff hist +135 Biostatistics 830 - Code Snippets →Code Snippets
• 14:5014:50, 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
• 14:4514:45, 25 September 2013 diff hist +33 Biostatistics 830 - Code Snippets →Code Snippets
• 14:4514:45, 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
• 14:4314:43, 25 September 2013 diff hist +36 Biostatistics 830 - Code Snippets →Code Snippets
• 14:4214:42, 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 < ..."
• 14:4114:41, 25 September 2013 diff hist +35 Biostatistics 830 - Code Snippets →Code Snippets
• 14:4014:40, 25 September 2013 diff hist −36 830 - MarkovModel::Condition() No edit summary current
• 14:4014:40, 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 ..."
• 14:4014:40, 25 September 2013 diff hist +1 Biostatistics 830 - Code Snippets →Code Snippets
• 14:4014:40, 25 September 2013 diff hist +35 Biostatistics 830 - Code Snippets →Code Snippets
• 14:3914:39, 25 September 2013 diff hist −202 830 - MarkovModel::Transpose() No edit summary current
• 14:3714:37, 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..."
• 14:3614:36, 25 September 2013 diff hist +2 Biostatistics 830 - Code Snippets →Code Snippets
• 14:3614:36, 25 September 2013 diff hist +34 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
• 14:3314:33, 25 September 2013 diff hist +72 Biostatistics 830: Main Page →Scheduling
• 14:3314:33, 25 September 2013 diff hist 0 N File:Question Sheet - Li et al (2010) Gen Epid.pdf No edit summary current
• 14:3214:32, 25 September 2013 diff hist +81 Biostatistics 830: Main Page →Class Worksheets
• 14:3214:32, 25 September 2013 diff hist 0 N File:Question Sheet - Howie et al (2012) Nat Genet.pdf No edit summary current
• 14:3114:31, 25 September 2013 diff hist +174 Biostatistics 830: Main Page →Scheduling
• 14:2914:29, 25 September 2013 diff hist 0 N File:Question Sheet - Browing and Browning (2012) Am J Hum Genet.pdf No edit summary current
• 11:0011:00, 25 September 2013 diff hist +208 Biostatistics 830 - Code Snippets →Howie et al (2012) Nat Genet
• 11:0011:00, 25 September 2013 diff hist +54 Biostatistics 830: Main Page →Required Reading
• 10:5910:59, 25 September 2013 diff hist +82 Biostatistics 830 - Code Snippets →Li et al (2010) Genet Epidemiol
• 10:5810:58, 25 September 2013 diff hist +1,613 Biostatistics 830: Main Page →Scheduling

13 September 2013

• 15:5615:56, 13 September 2013 diff hist −163 830 - Haplotyper::RandomSetup() No edit summary current
• 15:0715:07, 13 September 2013 diff hist +16 Biostatistics 830: Main Page →Required Reading
• 15:0615:06, 13 September 2013 diff hist −1 830 - Haplotyper::ImputeGenotypes() No edit summary
• 15:0615:06, 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..."
• 15:0415:04, 13 September 2013 diff hist +41 Biostatistics 830 - Code Snippets →Code Snippets
• 15:0215:02, 13 September 2013 diff hist +31 830 - Haplotyper::ScoreLeftConditional() No edit summary
• 15:0115:01, 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..."
• 15:0015:00, 13 September 2013 diff hist +46 Biostatistics 830 - Code Snippets →Code Snippets
• 14:5814:58, 13 September 2013 diff hist 0 830 - Haplotyper::ConditionOnData() No edit summary current
• 14:5814:58, 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 //..."
• 14:5614:56, 13 September 2013 diff hist 0 830 - Haplotyper::SetupPrior() No edit summary current
• 14:5614:56, 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 = ..."
• 14:5514:55, 13 September 2013 diff hist +77 Biostatistics 830 - Code Snippets →Code Snippets
• 14:5214:52, 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
• 14:4814:48, 13 September 2013 diff hist +1 Biostatistics 830 - Code Snippets →Code Snippets
• 14:4814:48, 13 September 2013 diff hist +34 Biostatistics 830 - Code Snippets →Code Snippets
• 14:4714:47, 13 September 2013 diff hist +91 830 - Haplotyper::RandomSetup() No edit summary
• 14:4614:46, 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..."
• 14:4214:42, 13 September 2013 diff hist +37 Biostatistics 830 - Code Snippets →Code Snippets
• 14:3814:38, 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..."
• 14:3714:37, 13 September 2013 diff hist +16 Biostatistics 830: Main Page →Required Reading
• 14:3714:37, 13 September 2013 diff hist +22 Biostatistics 830: Main Page →Required Reading

9 September 2013

• 10:5010:50, 9 September 2013 diff hist −2 Abecasis Group Awards No edit summary