FlxQTL.jl
A comprehensive package of Flexible multivariate linear (mixed) model (MLMM/MLM) for QTL (Quantitative Trait Loci) analysis of structured multivariate traits. Note that MLM-based scan functions can be used for a low heritability case for efficient computation.
Package Features
- Genome scans (1D, 2D) and permutation tests for univariate, multivariate trait(s), and genotype (probability) data
- LOCO (Leave One Chromosome Out) support for MLMM-based genome scans
- Computation for Genetic Relatedness matrix (GRM or kinship)
- CPU parallelization
Guide
Manual
The descriptions of functions and types arranged by module.
Index
FlxQTL.EcmNestrvFlxQTL.FlxQTLFlxQTL.GRMFlxQTL.MLMFlxQTL.UtilFlxQTL.flxMLMFlxQTL.flxMLMMFlxQTL.MLM.EstimatFlxQTL.Util.MarkersFlxQTL.GRM.kinship4wayFlxQTL.GRM.kinshipCtrFlxQTL.GRM.kinshipLinFlxQTL.GRM.kinshipLocoFlxQTL.GRM.kinshipManFlxQTL.GRM.kinshipStdFlxQTL.GRM.shrinkgFlxQTL.GRM.shrinkgLocoFlxQTL.MLM.mGLMFlxQTL.Util.Y_huberFlxQTL.Util.array2matFlxQTL.Util.getFinoidxFlxQTL.Util.getGenoidxFlxQTL.Util.lod2logPFlxQTL.Util.mat2arrayFlxQTL.Util.mat2vecFlxQTL.Util.newMarkersFlxQTL.Util.ordrMarkersFlxQTL.Util.setSeedFlxQTL.Util.sortBycMFlxQTL.flxMLM.mlm1ScanFlxQTL.flxMLM.mlm2ScanFlxQTL.flxMLM.mlmTestFlxQTL.flxMLMM.K2EigFlxQTL.flxMLMM.K2eigFlxQTL.flxMLMM.gene2ScanFlxQTL.flxMLMM.geneScanFlxQTL.flxMLMM.getKcFlxQTL.flxMLMM.permTest