Man pages for wolfemd/genomicMateSelectR
Genomic Mate Selection
| backsolveSNPeff | Compute ridge-regression equivalent marker effects from GBLUP... |
| calcCrossLD | Calculate the cross LD matrix based on both parents |
| calcGameticLD | Calculate the gametic LD matrix for a single parent |
| calcPropMissing | Calcluate the proportion missing data |
| centerDosage | Centers dosage matrix |
| compound | Assignment pipe |
| convertDart2vcf | Convert DArTseqLD reports to VCF |
| convertVCFtoDosage | Convert a VCF file to dosage matrix |
| createGenomewideDosage | Combine multiple dosage matrix to a single genome-wide dosage |
| crosses2predict | Make a data.frame of pairwise crosses between a set parents |
| curateTrialOneTrait | Fit model and remove outliers from one trial for one trait |
| curateTrialsByTrait | Fits mixed-models to each trial and all traits, removing... |
| detectExptDesigns | "Detect" experimental designs |
| dose2domDev | Converts a dosage matrix into a matrix of centered... |
| dose2domDevGenotypic | Converts a dosage matrix into a matrix of centered... |
| effectsArray2list | Converts an array of posterior samples of multi-trait marker... |
| exposition | Exposition pipe |
| filter_positions | Subset a VCF file based on provided positions |
| fitMultiTrialModel | Fit model and remove outliers from a multi-trial dataset |
| genmap2recombfreq | Create a matrix of pairwise recombination frequencies from a... |
| genomicMateSelectR-package | genomicMateSelectR: Genomic Mate Selection |
| genoVarCovarMatFunc | Compute the LD matrix from dosages |
| getAF | Compute allele frequencies |
| getMAF | Compute minor allele frequencies |
| getMarkEffs | Title |
| getPropHom | Compute the per-individual proportion homozygous |
| intensity | Standardized selection intensity |
| kinship | Construct several types of kinship matrix |
| maf_filter | Filter a dosage matrix by a minor allele frequency |
| makeParentFolds | Make parent-wise cross-validation folds |
| makeTrialTypeVar | Add TrialType classifier |
| meanPredAccuracy | Title |
| mergeVCFs | Merge two VCFs into one |
| nestByTrials | Nest data.frame by trials |
| nestDesignsDetectedByTraits | Set-up for a by-trait analysis downstream |
| nestForMultiTrialAnalysis | Restructure BLUPs for downstream analysis |
| nestTrialsByTrait | Nest trials by trait |
| pipe | Pipe operator |
| postImputeFilter | Apply quality filters after imputation by Beagle5.0 |
| postImputeFilterBeagle4pt1 | Apply quality filters after imputation by Beagle4.1 |
| predCrossMeans | Predict cross means |
| predCrossVars | Predict cross variances |
| predictCrosses | Predict crosses |
| predictCrossMeans | Title |
| predictCrossVars | Title |
| predOneCross | Title |
| predOneCrossVar | Title |
| quadform | Quadratic matrix form |
| readDBdata | Read database downloads into R |
| remove_invariant | Remove invariant SNPs from dosage matrix |
| renameAndSelectCols | Rename columns and remove everything unecessary |
| runBeagle4pt1GL | Run Beagle4.1 to impute a target VCF with a reference VCF |
| runBeagle5 | Run Beagle5 to impute a target VCF with a reference VCF |
| runCrossVal | Run k-fold cross-validation |
| runGenomicPredictions | Run genomic predictions |
| runParentWiseCrossVal | Run parent-wise cross-validation |
| splitVCFbyChr | Split a genome-wide VCF into separate chromosome-wise VCFs |
| varPredAccuracy | Title |
