man/User Manual.md

In YaoZhou89/BLINK: BLINK: A Package for Next Level of Genome Wide Association Studies with Both Individuals and Markers in Millions

How to run multiple traits?

BLINKR could only run one trait per time, if you want to run all trails in the myY, you can run like this:

for (i in 2:ncol(myY)){

  myBlink=Blink(Y=myY[,c(1,i)],GD=myGD,GM=myGM,maxLoop=10,time.cal=T,BIC.method="naive")

}

How to add coviates?

Note: the covriates file should be n by q, n is the individuals number and q is the number of covriates, and the order should be the same with myY and myGD. Like adding the top 3 PCs as coviates:

1. calculate PCs using prcomp:

cov = prcomp(as.matrix(myGD))

2. then extract the top 3 PCs:

myCV = cov$x[,1:3]
# if you only have one CV, the format should be matrix format. 
myCV = as.matrix(cov$x[,1])

3. run BLINK with PCs:

myBlink=Blink(Y=myY,GD=myGD,GM=myGM,CV = myCV, maxLoop = 10, time.cal = T)

Parameters may be useful

time.cal: calculate the time spend in each step;

maxLoop: the loop for iteration;

maf.threshold: filter SNPs with MAF < maf.threshold

YaoZhou89/BLINK documentation built on May 11, 2020, 7:22 p.m.