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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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LOH determined #69

Open Jingjiao-ma opened 6 years ago

Jingjiao-ma commented 6 years ago

Hi

 I run FACETS and get the results:
chrom   seg num.mark    nhet    cnlr.median mafR    segclust    cnlr.median.clust   mafR.clust  start   end cf.em   tcn.em  lcn.em
1   1   479 79  0.0965351900685901  0.0403774889537343  14  0.0486443901051894  0.0403774889537343  10583   581900  1   2   1
1   2   223937  35564   -0.260170210987769  0.240391887957227   3   -0.279420057298134  0.250369380666881   58230069426214  0.394624061086929   1   0
1   3   17560   2102    -0.369619979099715  0.252093019901172   2   -0.361566996656013  0.255944278101722   69426589    74757300    0.394624061086929   1   0
1   4   90955   13571   -0.31368627544908   0.253806864037177   3   -0.279420057298134  0.250369380666881   74757454    102153700   0.394624061086929   1   0

the ten.em=2 and lcn.em=0 is copy-neutral LOH state the ten.em=1 and lcn.em=0 is LOH or heterozygous deletions?

Best Regards~ Thank you !

veseshan commented 6 years ago

Heterozygous deletion is LOH i.e. what once was a het is no longer so.

Jingjiao-ma commented 6 years ago

Thank you, I kown the tcn.em=1 and lcn.em=0 is in LOH state.

dariober commented 6 years ago

...I just happened to see this thread... Maybe the table here helps to classify the CNV state into LOH, DEL, DUP etc...? (Scroll down a bit in the thread)

kobejamescurry commented 5 years ago

Heterozygous deletion is LOH i.e. what once was a het is no longer so. your LOH definition is not complete