Perform GWAS using FarmCPU method
MVP.FarmCPU(phe, geno, map, CV=NULL, priority="speed", P=NULL, method.sub="reward", method.sub.final="reward",
method.bin="EMMA", bin.size=c(5e5,5e6,5e7), bin.selection=seq(10,100,10), memo="MVP.FarmCPU",
Prior=NULL, ncpus=2, maxLoop=10, threshold.output=.01, converge=1, iteration.output=FALSE,
p.threshold=NA, QTN.threshold=NULL, bound=NULL)phenotype, n * 2 matrix
phenotype
genotype, n by m matrix. This is Genotype Data Pure (GD). THERE IS NOT COLUMN FOR TAXA.
SNP map information
covariates
speed or memory
a start p value for each SNP
method used in substitution process
EMMA or FaSTLMM
window size in genome
a vector, how many windows selected
a marker on output file name
four columns, SNP name, Chr, Pos, P
number of cpus used for parallele
maximum number of iterations
output GWAS results only for SNPs with p value lower than the threshold.output
an indicator for when loops stop
whether to output results for FarmCPU iterations
if all p values in the 1st iteration are bigger than p.threshold, FarmCPU stops
Only SNPs have a more significant p value than QTN.threshold have chance to be selected as pseudo QTNs
maximum number of SNPs selected as pseudo QTNs for each iteration