error running HLA-B

[mmaiers-nmdp]

I'm analyzing a cohort of N=79 for HLA-A, -B, -C, -DRB1 and -DQB1.

For HLA-B I get this error.

i can reproduce this error for HLA-A if I reduce the cohort to N=10 so it looks like it has something to do with the sample-size and diversity.

= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
          BIGDAWG: Bridging ImmunoGenomic Data Analysis Workflow Gaps
= = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = 

>>>>>>>>>>>>>>>>>>>>>>>>> BEGIN Analysis <<<<<<<<<<<<<<<<<<<<<<<<<

Data Input: df2 


>>>> DATA PROCESSING AND CHECKS.
Removing any missing data. This will affect Hardy-Weinberg Equilibrium test.

>>>> CASE - CONTROL SUMMARY STATISTICS
  Sample Summary
    Sample Size (n): 2 
    ...Number of Controls/Cases: 1/1 
    Allele Count (2n): 4 
    Total loci in file: 1 
    Unique loci: B 
    Unique alleles per locus: 4 
    ...Unique in Controls/Cases: 2/2 
    Missing alleles per locus: 0 
    ...Missing in Controls/Cases: 0/0 

  Observed Allele Resolution
    Max Resolution Controls: 2-Field 
    Max Resolution Cases: 2-Field 
    Defined Resolution: Not Defined 


>>>>>>>>>>>>>>>>>>>>>>>>> Begin Locus Sets <<<<<<<<<<<<<<<<<<<<<<<<<

Your analysis has 1 set to analyze.

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Running Set 1 

>>>> STARTING LOCUS LEVEL ANALYSIS...
> LOCUS LEVEL ANALYSIS COMPLETED 
 Locus X.square    df p.value   sig
     B    NCalc NCalc   NCalc NCalc


>>>>>>>>>>>>>>>>>>>>>>>>>> End Analysis <<<<<<<<<<<<<<<<<<<<<<<<<<
Error in bd$L$Set1$chisq$p.value : 
  $ operator is invalid for atomic vectors