ADDO_AddDom2_Pvalue: Detection and Classification of QTLs with Various Inheritance...

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

Description

Select significant QTLs using a matrix operation strategy and estimate the logP of each QTLs with 4 different models as well as their "tAdd" and "tDom" for inheritance categories classification. (1) Run the whole PLINK file or Run the separated PLINK files if the genotypes are massive ("Run_separated = F"); (2) Additive Recode Model (AA:0/AB:1/BB:2) vs Null Model; (3) Dominant Recode Model (AA:0/AB:1/BB:0) vs Null Model; (4) Add+Dom Recode Model (AA:0 0/AB:1 1/BB:2 0) vs Null Model; (5) Add+Dom Reocde Model (AA:0 0/AB:1 1/BB:2 0) vs Additive Model.

Usage

ADDO_AddDom2_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, matrix_acceleration = T, logP_threshold = 1,
  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.
matrix_acceleration	A logic variable. T: Implement the matrix acceleration to select significant loci before mixed model; F: Didn't implement the matrix acceleration.
logP_threshold	A numeric variable. The -logP threshold to select significant loci.
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_AddDom2_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.