gpwas: Genome-Phenome Wide Association Study

In shanwai1234/GPWAS: Genome-Phenome Wide Association Studies

Genome-Phenome Wide Association Study

Description

Genome-Phenome Wide Association Study

Usage

gpwas(ingeno, inpheno, inpc, g, gp, gv, R = num, pc = 3,
  selectIn = 0.01, selectOut = 0.01)

Arguments

ingeno	Input genotype file name/directory.
inpheno	Input phenotype file name/directory.
inpc	Input folder with PCA parsed population structure covariance. If n number of chromosomes, n number of separate files should be included, as SNPs on each chromosome is excluded for performing PCA once.
g	A list of specific gene that needs to analysis. By default the model will run for all of genes detected in the input genotype file.
gp	Output file name/directory for selected phenotypes with every gene as well as p value of each selected phenotype.
gv	Output file name/directory of terminated p value for each gene.
R	Number of iteration for scanning all of input phenotypes with one specific gene.
pc	Number of principle components that need to be included as covariances. Default is 3.
selectIn	P value threshold for considering a phenotype is significant to be included into the model. Default is 0.01.
selectOut	P value threshold for considering a phenotype is significant to be removed from the model. Default is 0.01.

Value

Two files with significance level per gene and selected phenotypes per gene

Examples

gpwas(ingeno,inpheno,inpc,g,gp,gv,R=35)

shanwai1234/GPWAS documentation built on Feb. 16, 2023, 3:15 a.m.