Function reference • genomicMateSelectR

Genomic mate selection functions Top level functions to predict the performance of individual genotypes and the usefulness of potential crosses.
`runGenomicPredictions()`	Run genomic predictions
`predictCrosses()`	Predict crosses
Cross prediction functions Behind-the-scenes functions that predict cross means and variances.
`predCrossVars()`	Predict cross variances
`predCrossMeans()`	Predict cross means
`calcGameticLD()`	Calculate the gametic LD matrix for a single parent
`calcCrossLD()`	Calculate the cross LD matrix based on both parents
Cross-validation functions Functions for automatically conducting cross-validation-based estimation of genomic prediction accuracy.
`runCrossVal()`	Run k-fold cross-validation
`runParentWiseCrossVal()`	Run parent-wise cross-validation
NextGen Cassava genomic selection Functions used in the standardized steps of the NextGen Cassava genomic selection breeding pipeline
Cassavabase phenotype data pipeline functions Functions for processing of cleaning and otherwise preparing field data.
`calcPropMissing()`	Calcluate the proportion missing data
`curateTrialOneTrait()`	Fit model and remove outliers from one trial for one trait
`curateTrialsByTrait()`	Fits mixed-models to each trial and all traits, removing outliers
`detectExptDesigns()`	"Detect" experimental designs
`fitMultiTrialModel()`	Fit model and remove outliers from a multi-trial dataset
`makeTrialTypeVar()`	Add TrialType classifier
`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
`readDBdata()`	Read database downloads into R
`renameAndSelectCols()`	Rename columns and remove everything unecessary
Imputation and Informatics Functions wrapping around standard command line bioinformatics tools, used for setting up and running imputation and post-imputation filtering on the genotypes needing prediction.
`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
`filter_positions()`	Subset a VCF file based on provided positions
`mergeVCFs()`	Merge two VCFs into one
`postImputeFilter()`	Apply quality filters after imputation by Beagle5.0
`postImputeFilterBeagle4pt1()`	Apply quality filters after imputation by Beagle4.1
`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
`splitVCFbyChr()`	Split a genome-wide VCF into separate chromosome-wise VCFs
Helper functions Support functions big and small!
`backsolveSNPeff()`	Compute ridge-regression equivalent marker effects from GBLUP results ("Backsolve SNP effects")
`centerDosage()`	Centers dosage matrix
`crosses2predict()`	Make a data.frame of pairwise crosses between a set parents
`dose2domDev()`	Converts a dosage matrix into a matrix of centered "classical"-coded dominance deviations.
`dose2domDevGenotypic()`	Converts a dosage matrix into a matrix of centered "genotypic"-coded dominance deviations.
`effectsArray2list()`	Converts an array of posterior samples of multi-trait marker effects to a named list (one for each trait).
`genmap2recombfreq()`	Create a matrix of pairwise recombination frequencies from a genetic map
`genoVarCovarMatFunc()`	Compute the LD matrix from dosages
`getAF()`	Compute allele frequencies
`getMAF()`	Compute minor allele frequencies
`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
`quadform()`	Quadratic matrix form
`remove_invariant()`	Remove invariant SNPs from dosage matrix

Reference

Genomic mate selection functions

Cross prediction functions

Cross-validation functions

NextGen Cassava genomic selection

Cassavabase phenotype data pipeline functions

Imputation and Informatics

Helper functions