Man pages for bahlolab/isoRelate
Identity-by-Descent Inference of Haploid Recombining Organisms
| AmatrixDD | The matrix A in the equation Ax=b for 2 diploid chromosomes |
| AmatrixHD | The matrix A in the equation Ax=b for 1 haploid and 1 diploid... |
| AmatrixHH | The matrix A in the equation Ax=b for 2 haploid chromosomes |
| annotation_genes | Plasmodium Falciparum Gene Annotation Dataset |
| areColors | Internal function |
| bVectorDD | The vector b in the equation Ax=b for 2 diploid chromosomes |
| bVectorHD | The vector b in the equation Ax=b for 1 haploid chromosome... |
| bVectorHH | The vector b in the equation Ax=b for 2 haploid chromosomes |
| calculateAlpha | Calculate alpha |
| calculateBeta | Calculate beta |
| calculateGamma | Calculate gamma |
| calculateLogLikelihood | Calculate the log-likelihood of the data |
| calculateMeiosis | Estimation of Meiosis |
| calculateMissingness | Calculate Missingness Proportions |
| calculatePopAlleleFreq | Calculate Allele Frequencies for SNPs from Genotype Data |
| calculateScale | Calculate scale |
| calculateViterbi | Calculate the Viterbi sequence |
| clusterSummary | A function that prints summary information of clusters |
| emissionProbDD | The emission probabilities for 2 diploid chromosomes |
| emissionProbHD | The emission probabilities for 1 haploid chromosome and 1... |
| emissionProbHH | The emission probabilities for 2 haploid chromosomes |
| emissionProbMissingGeno | Calculating the emission probability sumation when missing... |
| genotypeErrorD | The genotyping error probability for 1 diploid chromosome |
| genotypeErrorH | The genotyping error probability for 1 haploid chromosome |
| getColourPaletteMajor | IsoRelate Colour Palette for groups |
| getColourPaletteMinor | 'getColourPaletteMinor()' generates a specified number of... |
| getGenotypes | Pre-Analysis Data Processing |
| getIBDiclusters | Interval Cluster Networks |
| getIBDiR | Selection Significance Statistic |
| getIBDmatrix | Binary IBD Matrix |
| getIBDparameters | Parameter Estimation |
| getIBDpclusters | Genome Cluster Networks |
| getIBDposterior | IBD Posterior Probabilities |
| getIBDproportion | Proportion of Pairs IBD |
| getIBDsegments | IBD Segment Detection |
| getIBDsummary | IBD Segment Summary |
| getOverlap | function to find IBD that overlap interval |
| groupPairs | Group Combinations for Analysis |
| haplotypeToGenotype | Call Genotypes from Haplotype Data |
| highlight_genes | Plasmodium Falciparum Gene Highlight Dataset |
| IBDLabel | Internal Function |
| IBDMatrix | Binary Matrix of IBD |
| IBDparameters | IBDparameters() calculates IBD probabilities then estimates... |
| IBDTable | Internal Function |
| iRfunction | Internal Function |
| isolatePairs | Pair Combinations for Analysis |
| merge_lists | Internal Function |
| my_ibd | IBD Segments For The Papua New Guinea Dataset |
| plotIBDclusters | Plot Cluster Networks |
| plotIBDiR | Plot iR Statistics |
| plotIBDproportions | Plot The Proportion of Pairs IBD |
| plotIBDsegments | Plot IBD Segments |
| png_genotypes | Filtered Genotypes For The Papua New Guinea Dataset |
| png_ibd | IBD Segments For The Papua New Guinea Dataset |
| png_parameters | IBD Parameter Estimates For The Papua New Guinea Dataset |
| png_pedmap | Papua New Guinea Plasmodium Falciparum Dataset |
| roundDecimal | Round digits to specified decimal places |
| transitionProbDD | The transition probabilities for 2 diploid chromosomes |
| transitionProbHD | The transition probabilities for 1 haploid and 1 diploid... |
| transitionProbHH | The transition probabilities for 2 haploid chromosomes |
| trueGenotypes | Matrices of all possible genotype combinations between pairs,... |
