lassosum
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tshmak
LASSO for GWAS with summary statistics
Does pseudovalidate() also provide a valid estimate of corr(PRS, Phenotype) when there is no LD? That is, I'm simulating SNP data with no LD, then run a GWAS of a...
Hi, I ran the lassosum per chromosome using the multi-thread mode (10 threads). The code is as follows. `for (i in 1:22){ message(paste0("Chr ",i," is calculating")) ss
Hi, I ran the pipeline by chromosomes using the same ref.file and test.file for each chromosome, then merged the output variables together using "merge" in a loop. However, when I...
Dear tshmak Hello, I am running the lassosum.pipeline in unix but I have some errors related to this package. First chromosome-wise running is not working in some chromosomes. I am...
Hi @privefl , @tshmak I am benchmarking PRS/PGS methods practiced in the [PRS tutorial](https://choishingwan.github.io/PRS-Tutorial/). Regard to Lassosum, I got some confusions. I'd appreciate if you clarify them. Here they are:...
@tshmak thanks for the nice tool I have been using for a while I have these two snps in my summary stats which have really low pvalue and end up...
Hi, When I run the example of lassosum, it is difficult for me to get the same result from lassosum and plink. lassosum code is: ```` library(lassosum) setwd(system.file("data", package="lassosum")) ss
Hi, I have followed the suggestion to apply validated beta into new file as below out2 = subset(out, out$s=v$best.s, out$lambda=v$best.lambda) v2 = validate(out2, pheno=pheno.read[,3], covar = covar.read, test.bfile=newfile) At the...
Hi, I have applied the lassopipeline to a summary statitics and got a rds file succussefully, but when I run the pseudovalidate on a new data set (160K data) without...
Hey Tim, is there any documentation about the pseudovalidate? I am wondering what is the principle of pseudovalidate. By the way, can I use the same training dataset to do...
