Why the result of Froh_genome be the same as the result of Froh_Class_0 for each individual?

[ChaoXu1997]

In result_Froh_genome_wide and result_Froh_class, why should the result of Froh_genome be the same as the result of Froh_Class_0 for each individual?

[bunop]

dear @ChaoXu1997 can you provide some contextual information to your issue? can you reproduce the same behavior using test data?

[ChaoXu1997]

I encountered the same issue in the test data provided by the detectRUNS package.
R.version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
crt ucrt
system x86_64, mingw32
status
major 4
minor 2.2
year 2022
month 10
day 31
svn rev 83211
language R
version.string R version 4.2.2 (2022-10-31 ucrt)
nickname Innocent and Trusting

[bunop]

for what I understand, it seems to be related to this line in Froh_inbreedingClass function:

  Froh_Class=unique(runs[c('group','id')])
  for (i in range_mb[1:5]){
    print(paste("Class used: >",i,sep=''))

    # subset ROHom/ROHet
    subset_roh <- runs[runs$MB >= i,]

    #if subset is empty (no runs for that class) skip/continue
    if(nrow(subset_roh)<1) next

    Froh_temp <- ddply(subset_roh,.(id),summarize,sum=sum(lengthBps))
    Froh_temp[[paste("Froh_Class_",i,sep="")]] =  Froh_temp$sum/sum(LengthGenome$CHR_LENGTH)
    colnames(Froh_temp)[2]<- paste("Sum_Class_",i,sep="")
    Froh_Class=merge(Froh_Class,Froh_temp,by="id",all=TRUE)
  }

when i = 0 the subset_roh <- runs[runs$MB >= i,] will select the entire table, so the class 0 column will be equal to the total genome. Honestly, I can't tell you if this is a bug or not, and the code changed a lot from the version which is now uploaded in CRAN repository. @filippob , can you check this behavior please?