Error with Haplotypes

[cculma]

Hi, I have been using your package. The package works fine with my alfalfa dataset when I am using mpsnpdose format(0-4), however, when I try to use microhaplotypes (multiallelic markers), there is an error:

Haplotypes have been detected in the genotype matrix.
0 % missing genotypes detected.
No imputation will be performed.
No Q matrix will be used.
Linear model will be used.
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: non-numeric matrix extent

I can share my dataset to test the error. Thank you for your help!

Best,

Cesar

[cfljam]

Ive got the same issue....also keen to help with test data

[cfljam]

It turns out my problem was the presence of bi-allelic markers. This code reproduces the error

## Reproduce  mpQTL 'non-numeric matrix extent' error
library(mpQTL)
## Change a Marker to bi-allelic
mphapdose_bi <- copy(mphapdose)
mphapdose_bi['PotVar0071966',] <- sample(c(28,69),ncol(mphapdose),replace = T)

## fit linear model as per vignette with PotVar0071966 as a bi-allelic marker

print('fit linear model with PotVar0071966 as a bi-allelic marker')
lm2 <- mpQTL::map.QTL(
  phenotypes = mppheno,
  genotypes = mphapdose_bi,
  ploidy = 4,
  no_cores = 4,
  map = mpmap)

Output

[1] "fit linear model with PotVar0071966 as a bi-allelic marker"
Haplotypes have been detected in the genotype matrix.
0 % missing genotypes detected.
No imputation will be performed.
No Q matrix will be used.
Linear model will be used.
Error in checkForRemoteErrors(val) : 
  one node produced an error: non-numeric matrix extent

I was able to fit haplotype models once I had filtered bi-allelic markers out.

[alethere]

Thank you for sharing this issue (and the reproducible example).

Sorry for the late reply, but it is fixed. Biallelic haplotypes should no longer produce the error.

Cheers,
Alejandro

[cfljam]

Many thanks Alejandro!

[cfljam]

This update seems to have created a new issue

> library(mpQTL)
> result_dos <- map.QTL(phenotypes = mppheno,
+                       genotypes = mpsnpdose,
+                       ploidy = 4,
+                       map = mpmap)
SNP dosages have been detected in the genotype matrix,
0 % missing genotypes detected.
No imputation will be performed.
No Q matrix will be used.
Linear model will be used.
Error in get(name, envir = envir) : object 'w' not found