Open JohnHadish opened 4 years ago
Not sure why it is happening because this code from performBiasTests
should catch any edges where this is the case:
# Only perform the test if we have at least 10 samples in and
# out of the cluster.
if (length(non_cluster_samples) - length(missing_samples) >= 10 &
length(cluster_samples) >= 10) {
I have located the edge which is causing the issue:
Edge:
pycom06g10210 pycom05g21060 0.85556501 co 1 26 0011100000119100000010101000001011000009101100080191190000010111000001011100000 Tissue__Cortex 1.5652772e-11 nan
GEM for these genes:
pycom06g10210 11.4470832262097 11.6013065261218 12.062720767165 11.9038818457362 11.610563503925 11.1019756709492 10.9787104591064 11.4486325677306 11.1730524577741 11.3826240265749 11.891403996665 11.2149261879424 10.7431513941125 11.2597432636908 11.9307373375629 11.1535520317081 11.3179778224071 11.502334580198 11.2155329997457 11.2437690319619 11.7706638929168 12.0330788061306 11.5415806599912 11.9248125036058 12.0017600283272 10.9314762338868 10.9106427304696 11.2644426002266 11.5961897561444 11.0728025345442 12.2926092227643 11.7842258604263 11.2986354067342 11.9248125036058 11.2348174311173 11.8872206154684 11.4252159032994 11.856814552503 11.2969162068793 12.0320457269308 11.7494504655699 11.6429542234803 11.8776675740679 12.0484868739923 11.9549232920303 11.714674827308 11.6054795180617 10.642051692928 12.2626821423622 11.5294305541462 11.0084286220706 11.4696418172395 11.3944626946103 11.4252159032994 11.880348808156 11.523561956057 11.6564248632778 11.6794800995054 11.8447057644119 11.9516489859046 11.8649599151426 12.1497471195047 12.2224930522465 12.362765744154 11.9336906549522 11.8141818841903 11.8610869059954 11.8757493514201 11.6501542136751 12.0105281058865 12.0467829703564 11.5769566647061 12.0059753565004 11.8411711892485 11.4731983836775 11.7515440590891 11.6252522217469 11.9151324489507 11.6142497276894
pycom05g21060 2.32192809488736 1.58496250072116 2 2.32192809488736 1 6.97727992349992 6.91886323727459 7.53138146051631 7.03342300153745 6.8073549220576 1 0 -Inf 0 0 6.56985560833095 6.55458885167764 6.89481776330794 6.68650052718322 6.39231742277876 1.58496250072116 0 00 1 4.16992500144231 3.8073549220576 3.90689059560852 4.24792751344359 3.90689059560852 1.58496250072116 1 0 2 3.70043971814109 4.https://kinc.readthedocs.io/en/latest/16992500144231 4.52356195605701 4.32192809488736 4.16992500144231 -Inf 1 2 1 1.58496250072116 4.32192809488736 3.8073549220576 4 4.08746284125034 4.85798099512757 0 -Inf 0 1 -Inf 4.32192809488736 4.24792751344359 4.75488750216347 3.8073549220576 3.90689059560852 1 0 2.32192809488736 2.32192809488736 2.8073549220576 3.70043971814109 4.24792751344359 4.8073549220576 4.24792751344359 4.16992500144231 2.32192809488736 0 0 21 4.24792751344359 3.70043971814109 4.39231742277876 4.16992500144231 3.70043971814109
What ever edge immediatly follows this edge will throw the error. I am not sure why this is, but it prevents the program from running.
Example of "Network" (2 edges) which will fail:
Source Target Similarity_Score Interaction Cluster_Index Cluster_Size Samples Test_Name p_value r_squared
pycom06g10210 pycom05g21060 0.85556501 co 1 26 0011100000119100000010101000001011000009101100080191190000010111000001011100000 Tissue__Cortex 1.5652772e-11 nan
pycom06g10210 pycom05g21270 0.4647364 co 1 79 1111111111111111111111111111111111111111111111111111111111111111111111111111111 Ordinal 2.2092328e-12 0.5320459
Here are 2 more edges which broke this: Edge:
pycom17g10880 pycom01g00060 -0.88779348 co 1 17 0000000007000000070001108080000111008000911100080101910000011101000000001100000 Tissue__Cortex 6.3837683e-07 nan
GEM:
pycom17g10880 4.75488750216347 4 4.75488750216347 4.90689059560852 4 7.29462074889163 6.58496250072116 7.15987133677839 7.15987133677839 7.10852445677817 4.4594316186373 2.8073549220576 3.16992500144231 3.58496250072116 3.8073549220576 6.32192809488736 6 6.79441586635011 6.12928301694497 6.18982455888002 2.32192809488736 1 1.58496250072116 1 0 3.90689059560852 3.8073549220576 3.90689059560852 4.70043971814109 4.4594316186373 2 2.32192809488736 1.58496250072116 1.58496250072116 4.4594316186373 4.70043971814109 4.8073549220576 4.85798099512757 3.8073549220576 2.58496250072116 -Inf 1.58496250072116 1.58496250072116 1 4.85798099512757 4.58496250072116 4.52356195605701 3.70043971814109 5.24792751344359 1 0 1 -Inf 1.58496250072116 5.04439411935845 4.4594316186373 4.75488750216347 4.85798099512757 5.04439411935845 1.58496250072116 1.58496250072116 1 2.32192809488736 1 4.64385618977472 4.70043971814109 4.64385618977472 4.64385618977472 4.95419631038687 2 1.58496250072116 2.8073549220576 1.58496250072116 1 5 4.52356195605701 4.16992500144231 4.32192809488736 5.28540221886225
pycom01g00060 7.32192809488736 7.21916852046216 7.94251450533924 7.83289001416474 7.69348695749933 8.4178525148859 7.93073733756289 8.49984588708321 8.36632221424582 8.8073549220576 8.40514146313634 7.27612440527424 6.82017896241519 7.2667865406949 7.66533591718518 8.16992500144231 8.18487534290828 8.57742882803575 8.11374216604919 8.07681559705083 6.4594316186373 6.7279204545632 6.4757334309664 6.16992500144231 7.21916852046216 6.4594316186373 6 6.52356195605701 7.43462822763672 7.34872815423108 6.6724253419715 5.85798099512757 6.18982455888002 6.2667865406949 6.12928301694497 6.98868468677217 7.25738784269265 7.4757334309664 6.94251450533924 6.4093909361377 6.7279204545632 6.2667865406949 6.2667865406949 6.93073733756289 6.76818432477693 6.58496250072116 6.71424551766612 5.39231742277876 7.21916852046216 6.75488750216347 6.02236781302845 6.84549005094437 6.39231742277876 5.95419631038687 6.91886323727459 6.4594316186373 6.8073549220576 6.44294349584873 6.85798099512757 6.02236781302845 6.08746284125034 6.55458885167764 6.55458885167764 6.85798099512757 6.64385618977472 6.64385618977472 6.44294349584873 6.59991284218713 6.2667865406949 6.62935662007961 6.85798099512757 6.53915881110803 6.4594316186373 6.98868468677217 6.71424551766612 6.33985000288462 6.53915881110803 6.5077946401987 6.32192809488736
Edge:
pycom15g16080 pycom14g02680 0.71663702 co 2 28 7707900000007000000011110000001111000001111100000111110000011111000001111100000 Tissue__Cortex 8.86006e-13 nan
GEM:
pycom15g16080 0 1 1.58496250072116 1 -Inf 3.4594316186373 2.58496250072116 3.32192809488736 2.8073549220576 1.58496250072116 3.70043971814109 2 1 2.32192809488736 2 3.58496250072116 3.4594316186373 3.4594316186373 3 1.58496250072116 5.93073733756289 6.16992500144231 4.75488750216347 5.32192809488736 4.64385618977472 5.35755200461808 4.52356195605701 4.4594316186373 4.70043971814109 4.52356195605701 7.68650052718322 7 6.74146698640115 6.98868468677217 5.8073549220576 6.14974711950468 5 6.4093909361377 5.93073733756289 6.59991284218713 6.12928301694497 6.90689059560852 6.58496250072116 6.7279204545632 5.83289001416474 5.4594316186373 5.58496250072116 4.85798099512757 6.44294349584873 7.32192809488736 7.19967234483636 6.98868468677217 6.70043971814109 7.14974711950468 6.78135971352466 6.4594316186373 7.28540221886225 6.08746284125034 6.4757334309664 5.88264304936184 5.88264304936184 5.90689059560852 6.58496250072116 7 5.4262647547021 5.8073549220576 5.70043971814109 5.93073733756289 5.8073549220576 6.68650052718322 6.90689059560852 7.21916852046216 7.60733031374961 7.61470984411521 7.12928301694497 7.06608919045777 6.95419631038687 7.36632221424582 6.55458885167764
pycom14g02680 1 0 1.58496250072116 3.16992500144231 2 6.56985560833095 6.39231742277876 7.08746284125034 6.62935662007961 6.55458885167764 2 1.58496250072116 1 1.58496250072116 2.8073549220576 6.06608919045777 5.61470984411521 6.16992500144231 5.7279204545632 5.75488750216347 1.58496250072116 2 0 12.32192809488736 5.28540221886225 5.61470984411521 5.28540221886225 5.24792751344359 5.16992500144231 2.8073549220576 2 1.58496250072116 1.58496250072116 5.58496250072116 5.64385618977472 5.28540221886225 6.18982455888002 5.7279204545632 1.58496250072116 1.58496250072116 1.58496250072116 1 2 6.39231742277876 6.02236781302845 5.8073549220576 5.12928301694497 7.06608919045777 2.58496250072116 2 1 0 2 6.4262647547021 6.2667865406949 6.61470984411521 6.24792751344359 6.4594316186373 1 0 0 0 2 6.55458885167764 6.58496250072116 6.18982455888002 6.02236781302845 6.35755200461808 0 2.8073549220576 2 1.58496250072116 2.8073549220576 6.44294349584873 6.8703647195834 6.75488750216347 6.74146698640115 6.62935662007961
This appears to be an issue with too few samples in the out cluster. I am going to redo this run but with output that can identify the edge which it failed on.