Man pages for laurentlab-mpipz/rsurvival
Process genotype data from survival experiment
| AnalyseExpt | A function to analyse a selection experiment, including... |
| AnalyseSplittedExpt | A function to analyse a selection experiment, including... |
| CalcFreqGt | A function to count occurences of genotypes in a genotype... |
| CalcFreqVariant | A function to count occurences of genotypes in a variant... |
| CalcOddedPick | A function to calculate the number of picked lives per... |
| CalcOddsPredation | A function to calculate odds for predation from observed... |
| CalcProbsSelection | A function to calculate probabilities that observed... |
| CensorLowDepth | A function to replace genotype data with low depth by NA |
| ConvertFileToLogic | A function to turn a file into a logical vector. Useful for... |
| CountSignSnps | A function to count snps with a low probability of being due... |
| EstimateFST | A function to estimate the FST of a variant using the Weir &... |
| ExtractGt | A function to extract a genotype from a vcfR::VCF object. |
| FindIdsAlFreqs | A function to find the ids of freq.al columns in a frequency... |
| FindIdsGtCounts | A function to find the ids of counts.gt columns in a... |
| IsAtLeastNARatio | A function to check if the ratio of NA in a vector is over a... |
| IterRandPick | A function to iterate significant snps counting in a genotype... |
| LoadVcf | A function to get a filtered (and possibly splitted)... |
| OmitPoorSamples | A function to remove columns with a high ratio of missing... |
| OmitPoorVariants | A function to remove rows with a high ratio of missing data... |
| PermutRandSurv | A function to calculate probabilities of neutral model and... |
| RmIndels | A function to remove indel variants from a vcfR::VCF object |
| RmNonBiallelics | A function to remove non-biallelic variants from a vcfR::VCF... |
| SliceDfColumns | A function to slice data frames without loosing column names |
| SliceDfRows | A function to slice data frames without loosing row names |
| SplitGt | A function to split a genotype matrix two genotype matrix... |
| SplitVcf | A function to split a vcfR::VCF object in two vcfR::VCF... |
| SplitVect | A function to split a vector into two vectors according to a... |
