snpnet
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junyangq
snpnet: Fast and scalable lasso/elastic-net solver for large SNP data
I'm trying to run snpnet on UK Biobank data with 340K indivs and 500K variants (pgen is only 22GB). I use nodes with 16 cores and 128 GB RAM. I...
Hi, I notice that BASIL is a framework for large-scale LASSO of any distribution, and could be applied to continuous variables. So aside from snpnet which is designed for genotype...
When trying to run `snpnet`, `computeStats` fails with ``` Error: Problem with `mutate()` column `stats_means`. ℹ `stats_means = (HAP_ALT_CTS + HET_REF_ALT_CTS + 2 * TWO_ALT_GENO_CTS)/OBS_CT`. ✖ non-numeric argument to binary...
I guess it comes from https://github.com/junyangq/snpnet/blob/master/R/functions.R#L426.
Do you recommend pruning the UKBB genotype data to some extent before running or just running on all of the variants?
I am using the snpnet software to handle the UK biobank BMI data. It seems stuck at the step "Extracting number of variants and colnames from train.bim" for a long...
Hi, I wonder how to run snpnet without penalizing covariates? I can see [here](https://rdrr.io/github/junyangq/snpnet/man/snpnet.html) that in `snpnet()`, argument `p.factor` can be used to control penalization and there it says that...
