Description Usage Arguments Value Examples
This function tests a specific gene using summary statistics (score vector and its covariance matrix)
1 | FST.SummaryStat.test(score,Sigma,Z,weights,B=5000)
|
score |
The score vector of length p, where p is the total number of genetic variables. |
Sigma |
The p*p covariance matrix of the score vector |
Z |
Functional annotation scores, an p*q matrix where p is the total number of genetic variables and q is the number of functional annotation scores. Note that the first column in Z should be all 1 if the users want the original weights of SKAT/burden test to be included. |
weights |
A numeric vector of weights for genetic variants (The length should be same as the number of genetic variants in the set.). These weights are usually based on minor allele frequencies. |
B |
Number of Bootstrap replicates. The default is 5000. |
p.value |
P-value of the set based generalized score type test. |
1 2 3 4 5 6 7 8 9 10 | ## FST.SummaryStat.test tests a region.
# Input: score (a score vector), Sigma (the covariance matrix of the score vector)
library(FSTpackage)
data(FST.example)
score<-FST.example$score;Sigma<-FST.example$Sigma;Z<-FST.example$Z;weights<-FST.example$weights
# test with 5000 bootstrap replicates
result<-FST.SummaryStat.test(score,Sigma,Z,weights,B=5000)
|
Loading required package: CompQuadForm
Loading required package: SKAT
Loading required package: Matrix
Loading required package: MASS
Loading required package: mvtnorm
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.