search

kbroman / qtl

R/qtl: A QTL mapping environment
https://rqtl.org
GNU General Public License v3.0
77 stars 45 forks source link

Problem in scantwo permutations #94

Closed kbroman closed 11 months ago

kbroman commented 3 years ago

A problem with scantwo permutations was reported at the R/qtl google group:

I have a problem running scantwo with n.perm>0 (e.g n.perm=10) when I use this code-

mycross<-calc.genoprob(mycross,2,map.function="kosambi")
operm2<-scantwo(mycross,pheno.col=c(7:8),method="hk",n.perm=10)

I get the error-

Permutation 1 
Error in dimnames(out$lod) <- `*vtmp*` : 'dimnames' applied to non-array

mycross info-

  147  individuals
  3036  markers
  14  phenotypes
 --Cross type: f2

It used to work but since I run the script with n.cluster=2 as a local job, the error popped up-

Error in checkForRemoteErrors(val) : 
  2 nodes produced errors; first error: 'dimnames' applied to non-array
Calls: sourceWithProgress ... clusterApply -> staticClusterApply -> checkForRemoteErrors
Execution halted
kbroman commented 11 months ago

Without further information, this is not reproducible, and I'm going to close the issue.