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Error in splitvec.from.bfile(bfile) : length(pvec) == length(bfile) is not TRUE #43
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Can you give me your entire script? |
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So are you still getting this error |
I don't get this error anymore when I do validate(out) where "out <- merge(out1, out2, out3...out22)". The error occured previously when I do validate(out) where out is merged by each of the lassosum.poipeline output from chromosomes in a for loop as shown in the code above. Sorry about the confusion, my current question is which validatation method to use for large samples. I have 400k samples for matched genotype and phenotype, and the previous run with validate(out, pheno,covar) has ran over 9 hours with 40 cores. I was wondering if this is normal behaviour, or is there a better way to parallelise it? |
Yes, calculating PGS can take a long time with a large sample size. One way to speed up the calculation is to use multiprocessing (see here). Another way is to try to ensure the covar and the pheno is in the exact order as test.bfile. (Maybe you need to ensure there are no missing values also, but I can't remember if that's the case.) If everything matches exactly, you will not see the message |
Thanks very much, |
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 used "validate", it threw the error:
Error in splitvec.from.bfile(bfile) :length(pvec) == length(bfile) is not TRUE
Could you explain to me what might caused the error?
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