Comments (3)
For a FBM (the format used to store the genotype matrix G
), you can convert it to a standard R matrix with G[]
.
Beware of the memory then.
from bigstatsr.
Hi to all,
I read the data using the bigsnpr package using these codes.
- extdata="E:\Running\data"
- (bedfile <- system.file("extdata", "mydata.bed", package = "bigsnpr"))
- rds <- snp_readBed(bedfile, backingfile = tempfile())
After running the last line I get the following error:
Error: Path ' ' must have 'bed' extension.
My directory (extdata) contains the plink files. How to solve this error?
Thank you in advance!
from bigstatsr.
Do not use system.file(), it is used to access a path installed in a package.
Just provide the path directly between quotes.
from bigstatsr.
Related Issues (20)
- Support for character type data? HOT 1
- OpenMP flag is not passed HOT 19
- Estimation of model performance HOT 1
- Predicting using only 1 specific lambda value HOT 2
- Fixed and random effect HOT 6
- Perform `colSums(X^2)` on FBM object HOT 2
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- How to get p-value out of gwas<-big_univLinReg(...) object? HOT 10
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- How to cbind/rbind two big matrices that have the same dimension HOT 9
- Issues with locking of the backing file HOT 6
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- Scaling predictor variables both in training and test datasets HOT 5
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from bigstatsr.