ScoreEB {ScoreEB}

Score Test Integrated with Empirical Bayes for Association Study

Description

Perform association test within linear mixed model framework using score test integrated with Empirical Bayes for genome-wide association study. Firstly, score test was conducted for each marker under linear mixed model framework, taking into account the genetic relatedness and population structure. And then all the potentially associated markers were selected with a less stringent criterion. Finally, all the selected markers were placed into a multi-locus model to identify the true quantitative trait nucleotide.

Usage

ScoreEB(genofile, phenofile, popfile = NULL, trait.num = 1, EMB.tau = 0,
EMB.omega = 0, B.Moment = 20, tol.pcg = 1e-4, iter.pcg = 100, bin = 100,
lod.cutoff = 3.0, seed.num = 10000, dir_out)

Arguments

genofile

Genotype file name, change the file path where it is located, i.e.,"D:/Genotype_Example.csv".

phenofile

Phenotype file name, change the file path where it is located, i.e.,"D:/Phenotype_Example.csv".

popfile

Population structure file name, change the file path where it is located,i.e.,"D:/Population.csv".

trait.num

trait.num stands for computing trait from the 1st to the "trait.num"

EMB.tau

EMB.tau and EMB.omega are two values of hyperparameters in empirical Bayes step, which are set to 0 by default.

EMB.omega

As describe in EMB.tau

B.Moment

B.Moment is a parameter to obtain trace of NxN matrix approximately using method of moment. B.Moment is set to 20 by default.

tol.pcg

tol.pcg and iter.pcg are tolerance and maximum iteration number in preconditioned conjugate gradient algorithm.

iter.pcg

As describe in tol.pcg

bin

bin is to choose the maximum score within a certain range.

lod.cutoff

lod.cutoff is the threshold to determine identified QTNs.

seed.num

Set a random number.

dir_out

Give the path where it will be saved,i.e.,"D:/Result"

Value

result.total

A data frame of identified markers, including "Trait", "Id", "Chr", "Pos", "Score", "Beta", "Lod" and "Pvalue" of markers.

Note

1. genofile and phenofile are the required input file, while popfile is the optional input file.
2. In the "tempdir()" folder, there are two results files "ScoreEB.Result.csv" and "ScoreEB.time.csv" generated and saved after the run.
3. The results file "ScoreEB.Result.csv" has 8 columns, including "Trait", "Id", "Chr", "Pos", "Score", "Beta", "Lod" and "Pvalue".
4. The time file "ScoreEB.time.csv" includes 3 rows, which are "User", "System", "Elapse" time, respectively.

Author(s)

Wenlong Ren
Wenlong Ren <[e-mail]>

Examples

genofile <- system.file("extdata", "Genotype_Example.csv", package="ScoreEB")
phenofile <-system.file("extdata", "Phenotype_Example.csv", package="ScoreEB")
dir_out <- tempdir()
ScoreEB(genofile, phenofile, popfile = NULL, trait.num = 1, EMB.tau = 0,
EMB.omega = 0, B.Moment = 20, tol.pcg = 1e-4, iter.pcg = 100, bin = 100,
lod.cutoff = 3.0, seed.num = 10000, dir_out)