ADDO_Heterotic2_Pvalue: Pvalue calculation and Verfication of Overdominance QTLs...

In LeileiCui/ADDO: a comprehensive toolkit to detect, classify and visualise additive and non-additive Quantitative Trait Loci

Description

P-value Calculation and Verfication of overdominance (or heterotic) QTLs (1) Run the whole PLINK file or Run the separated PLINK files ("Run_separated = F"); (2) Indicate Reocde Model (AA:1 0 0/AB:0 1 0/BB:0 0 1) without the "1" column of covariance matrix; (3) Estimate two T-statistics (t(AB-AA) and t(AB-BB)) to measure the deviation between the effect of heterozygote (AB) and that of two homozygotes (AA and BB); (4) Generate the P-value based on MVN distribution using the minor(abs(t(AB-AA)),abs(t(AB-BB))) from SNPs with t(AB-AA)*t(AB-BB)>0.

Usage

ADDO_Heterotic2_Pvalue(indir = indir, outdir = outdir,
  Input_name = Input_name, Kinship_type = Kinship_type,
  VarComponent_Method = VarComponent_Method, PheList_Choose = F,
  PheList = PheList, Phe_HistogramPlot = F, Run_separated = F,
  covariates_sum = covariates_sum, Phe_IndMinimum = 200,
  GT_IndMinimum = 10, num_nodes = 10)

Arguments

indir	A character. The input directory where contains the input bPLINK or GenABEL data.
outdir	A character. The output directory where generates the folder: "2_Pvalue".
Input_name	A character. The prefixes of the input files.
Kinship_type	A character. The method to generate kinship matrix. Please select from "GenABEL","EMMA","EMMAX","GEMMA", "GCTA", "GCTA_ad", "HOMEBREW_AFW" or "HOMEBREW_AS".
VarComponent_Method	A character. The method to estimate variance components. Please select from "EMMA_a", "GCTA_a" or "GCTA_ad" (When VarComponent_Method is "GCTA_ad", the Kinship_type must be "GCTA_ad").
PheList_Choose	A logic variable. T: Just investigate specified phenotypes; F: Investigate all phenotypes.
PheList	A vector of character. When choose "PheList_Choose=F", the specified phenotype list must be specified.
Phe_HistogramPlot	A logic variable. T: Draw the histogram plots for all phenotypes; F: Aviod the histogram plots.
Run_separated	A logic variable. T: Run the separated genotype files; F: Run the whole genotype file.
covariates_sum	A numeric variable. The sum of all covariates.
Phe_IndMinimum	A numeric variable. Remove phenotypes without enough available individuals.
GT_IndMinimum	A numeric variable. Remove loci with available individuals <GT_IndMinimum for all three genotypes.
num_nodes	A numeric variable. The number of cores used parallelly.

Value

a folder named "2_Pvalue" with various statistics of each significant SNP for all phenotypes.

Author(s)

Leilei Cui and Bin Yang

Examples

ADDO_Heterotic2_Pvalue(indir=indir, outdir=outdir, Input_name="TEST", Kinship_type="GCTA_ad", VarComponent_Method="GCTA_ad", covariates_sum=2)

LeileiCui/ADDO documentation built on July 25, 2020, 1:51 a.m.