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A question about FarmCPU #88

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z4668640 opened this issue Aug 22, 2023 · 3 comments
Closed

A question about FarmCPU #88

z4668640 opened this issue Aug 22, 2023 · 3 comments

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@z4668640
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At present, when I use 'rmvp', I always encounter an error as follows, I want to know why? How to solve it?
R: 4.3.1
rMVP: 1.0.6

for (i in 2:ncol(phenotype)) {
  imMVP <- MVP(
    phe = phenotype[, c(1, i)],
    geno = genotype,
    map = map,
    K = Kinship,
    CV.GLM = Covariates_PC,
    CV.MLM = Covariates_PC,
    CV.FarmCPU = Covariates_PC,
    nPC.GLM = 5,
    nPC.MLM = 3,
    nPC.FarmCPU = 3,
    priority = "speed",
    #ncpus=10,
    vc.method = "BRENT",
    maxLoop = 10,
    method.bin = "FaST-LMM",
    #permutation.threshold=TRUE,
    #permutation.rep=100,
    threshold = 0.05,
    method = c("GLM", "MLM", "FarmCPU"),
    file.output = TRUE
  )
  gc()
}

FarmCPU Start... 
Current loop: 1 out of maximum of 10 
seqQTN: 
NULL 
number of covariates in current loop is: 
8 
scanning... 
[>>>----------------------------------------->] TimeLeft: 0s  
Current loop: 2 out of maximum of 10 
Optimizing Pseudo QTNs... 
Error in !is.null(snp.pool) && var(snp.pool) == 0 : 
  'length = 100' in coercion to 'logical(1)'
@XiaoleiLiuBio
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Thank you for reporting this issue. This is a problem caused by the new R version, we will update the package soon.

@XiaoleiLiuBio
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We have updated rMVP to 1.0.7 to solve the problem and fixed some known issues.

@z4668640
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z4668640 commented Sep 2, 2023

We have updated rMVP to 1.0.7 to solve the problem and fixed some known issues.

Thank you very much. I'll try it soon.

@z4668640 z4668640 closed this as completed Sep 2, 2023
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