Table 1 Overview of main polyRAD functions
Import functions
VCF2RADdataImports any VCF with an allelic read depth (AD) field, such as those exported by TASSEL-GBSv2 or GATK.
readTagDiggerImports CSV file of read depth output by TagDigger.
readStacksReads catalog and matches files from Stacks.
readTASSELGBSv2Reads SAM and TagTaxaDist files from TASSEL-GBSv2.
readHMCReads files output by UNEAK.
Genotype estimation functions
PipelineMapping2ParentsFor mapping populations with any number of generations of backcrossing, intermating, and/or selfing.
IterateHWEFor diversity panels without population structure.a
IterateHWE_LDFor diversity panels with LD and without population structure.a
IteratePopStructFor diversity panels with population structure.a
IteratePopStructLDFor diversity panels with population structure and LD.a
Export functions
ExportGAPITFormat genotypes for the GD and GM arguments of GAPIT or FarmCPU.
Export_rrBLUP_AmatFormat genotypes for the A.mat function in rrBLUP.
Export_rrBLUP_GWASFormat genotypes for the GWAS function in rrBLUP.
Export_TASSEL_NumericWrite file formatted for TASSEL with continuous numeric genotypes.
Export_polymapRFormat genotypes for the polymapR package.
GetWeightedMeanGenotypesCreate a matrix of continuous numeric genotypes.
GetProbableGenotypesCreate a matrix of discrete genotypes, indicating the most probable genotype for each individual and allele.
  • a The rate of self-fertilization can be specified for self-compatible plant species.