Object 1: To perform GWAS using General Linear Model (GLM), Mixed Linear Model (MLM), and FarmCPU model Object 2: To calculate kinship among individuals using Varaden method Object 3: Estimate variance components using EMMA, FaST-LMM, and HE regression Object 4: Generate high-quality figures
MVP(phe, geno, map, K=NULL, nPC.GLM=NULL, nPC.MLM=NULL, nPC.FarmCPU=NULL,
perc=1, CV.GLM=NULL,CV.MLM=NULL, CV.FarmCPU=NULL, REML=NULL,
priority="speed", ncpus=2, vc.method="EMMA",method="MLM", maxLine=1000,
memo="MVP", P=NULL, method.sub="reward", method.sub.final="reward",
method.bin="static",bin.size=c(5e5,5e6,5e7),bin.selection=seq(10,100,10),
Prior=NULL,maxLoop=10, threshold.output=1, iteration.output=FALSE,
p.threshold=NA, QTN.threshold=NULL,bound=NULL, outward=TRUE,
col=c("dodgerblue4","olivedrab4","violetred","darkgoldenrod1","purple4"),
plot.type="b", file.output=TRUE, file="jpg", dpi=300, threshold=0.05,
Ncluster=1, signal.cex=0.8)phenotype, n * 2 matrix, n is sample size
Genotype in bigmatrix format; m * n, m is marker size, n is sample size
SNP map information, SNP name, Chr, Pos
Kinship, Covariance matrix(n * n) for random effects, must be positive semi-definite
number of PCs added as fixed effects in GLM
number of PCs added as fixed effects in MLM
number of PCs added as fixed effects in FarmCPU
percentage of total SNPs selected for PCA
covariates added in GLM
covariates added in MLM
covariates added in FarmCPU
a list contains ve and vg
speed or memory
number of cpus used for parallel
methods for estimating variance component("EMMA" or "GEMMA")
the GWAS model, "GLM", "MLM", and "FarmCPU", models can be selected simutaneously, i.e. c("GLM", "MLM", "FarmCPU")
when the priority is 'memory', users can change this parameter to limit the memory
a marker added on output file name
a start p value for each SNP
method used in substitution process
method used in substitution process
EMMA or FaSTLMM
window size in genome
a vector, how many windows selected
four columns, SNP name, Chr, Pos, P
maximum number of iterations
output GWAS results only for SNPs with p value lower than the threshold.output
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
the direction of circular Manhattan plot
for color of points in each chromosome on manhattan plot
if use a permutation cutoff or not (bonferroni cutoff)
number of permutation replicates
"b" (both Manhattan plot and qq plot will be draw) or "q" (qq plot only)
whether to output files or not
figure format, "jpg", "tiff"
resolution
a cutoff line on manhattan plot, 0.05/marker size
number of colors used for drawing PC 1 and PC 2
point size on output figures
| Package: | MVP |
| Type: | Package |
| Version: | 1.0.1 |
| Date: | 2017-12-12 |
| License: | GPL(>=2) |