bigsnpr
bigsnpr copied to clipboard
privefl
R package for the analysis of massive SNP arrays.
Hi, I'm trying to work with the imputed data from UK Biobank. I'm using the RStudio workbench through dnanexus (as data can't be downloaded). I keep running into errors with...
Hi Florian, I'm using the following codes to obtain the final model summary and I have some troubles as my target variable is binary. Can you suggest how I can...
Hi! I need to generate the LD reference but the "snp_asGeneticPos" kept giving the same error message every time. I tried different versions of R and different input datasets, including...
e.g. -1.000......04
Hi Florian, Thanks for making this nice package. I added a function to compute genetic correlation using cross-trait LDSC. Here are the changes I made: - Added function `snp_ldsc_rg` for...
`spline()` will complain about non-monotonous inputs otherwise. Tested on the provided list of hm3 variants map.rds (https://ndownloader.figshare.com/files/25503788)
E.g. via a `snp_readPgen()` function analogous to `snp_readBed()`. The plink2 binary format (https://www.cog-genomics.org/plink/2.0/input#pgen) has several advantages over the plink1 binary format (bed/bim/fam): - Data are stored as probabilistic dosages, rather...
Currently, lambda_GC(X2) = lambda_GC(Z)^2. This can be confusing when comparing Q-Q plots using different statistics. What to do about it?
Count missing values as 0, and divide by the proportion of non-missing values.
In `snp_fastImpute()` and `snp_fastImputeSimple()`, warn when a variant has e.g. more than 20% missing values. These two functions are designed to impute genotyping arrays with a few missing values, and...