plotMixure() fails on LOH S4 object

[lindsay-liang]

Hi all,

Thank you so much for your work on madseq! I ran madseq on a whole exome sequencing sample and for chr7, runMadseq selected LOH as the correct model. However plotMixture() on the object returned by runMadseq fails with the following error:

> plotMixture(child_aneu_chr)
Error in plot.window(...) : need finite 'ylim' values

Here's the head of the s4 object:

> child_aneu_chr
MadSeq object with the posterior distribution from LOH model
         cgp1     cgp2        d1        d2         f    kappa         m    m_cov      p_cov    r_cov
[1,] 310.3821 480.6496 0.1332500 0.1233063 0.2619066 29.45540 0.4260071 69.17116 0.08973430 6.818916
[2,] 311.2032 480.2347 0.1217332 0.1133802 0.2400742 27.48999 0.4260071 69.17116 0.09029787 6.865993
[3,] 311.7972 480.3603 0.1363514 0.1259575 0.2677609 27.28657 0.4260071 69.17116 0.08971002 6.816889
[4,] 307.7333 479.9369 0.1181464 0.1102624 0.2332447 23.00610 0.4260071 69.17116 0.09190251 7.000353
[5,] 307.4564 479.3270 0.1287741 0.1194638 0.2534390 24.10222 0.4260071 69.17116 0.09323694 7.112450
[6,] 307.6737 481.4371 0.1140054 0.1066472 0.2253421 23.78006 0.4260071 69.17116 0.09294114 7.087573
------
            BIC_LOH          BIC_normal        BIC_monosomy BIC_mitotic_trisomy BIC_meiotic_trisomy 
            0.00000            39.91419            58.69772            62.88978           241.83324 

And from digging around in the code (PlotShow.R) it looks like all of the variables going into determining the y-axis (a1-a4, b1-b4, p1-p4, m1-m3) are all NA; is the s4 object malformed or is the issue in plotMixture()?

Please let me know if I can provide anything else to help debug!