gpwas | R Documentation |
Genome-Phenome Wide Association Study
gpwas(ingeno, inpheno, inpc, g, gp, gv, R = num, pc = 3, selectIn = 0.01, selectOut = 0.01)
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. |
Two files with significance level per gene and selected phenotypes per gene
gpwas(ingeno,inpheno,inpc,g,gp,gv,R=35)
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