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fpbarthel / GLASS

GLASS consortium
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dNdsCV WGS vs WXS discrepancy #114

Closed fpbarthel closed 5 years ago

fpbarthel commented 5 years ago

Noticed that there was a significant WGS - WXS discrepancy in dNdS values:

WGS only - all

> print(dnds_all$globaldnds)
     name       mle     cilow    cihigh
wmis wmis 0.9038689 0.8572250 0.9530508
wnon wnon 1.0262582 0.9031470 1.1661512
wspl wspl 0.8683643 0.7285441 1.0350185
wtru wtru 0.9682232 0.8700129 1.0775198
wall wall 0.9103546 0.8640947 0.9590911
> print(dnds_all$nbreg$theta)
[1] 1.164236

WXS only - all

> print(dnds_all$globaldnds)
     name      mle     cilow   cihigh
wmis wmis 1.090248 1.0504787 1.131522
wnon wnon 1.090733 0.9970975 1.193162
wspl wspl 1.224827 1.0924622 1.373229
wtru wtru 1.137321 1.0568157 1.223959
wall wall 1.093183 1.0538020 1.134035
> print(dnds_all$nbreg$theta)
[1] 2.108167

However, after running each separately by fraction, the results are similar to the overall results.

WGS only - by fraction

> print(dnds_shared$globaldnds)
     name      mle    cilow   cihigh
wmis wmis 1.179658 1.042734 1.334562
wnon wnon 1.524664 1.159204 2.005343
wspl wspl 1.461381 1.020414 2.092910
wtru wtru 1.501752 1.195350 1.886693
wall wall 1.204635 1.066531 1.360623
> print(dnds_primary$globaldnds)
     name      mle     cilow   cihigh
wmis wmis 1.018845 0.9262515 1.120694
wnon wnon 1.214976 0.9852547 1.498260
wspl wspl 1.211292 0.9074700 1.616835
wtru wtru 1.213756 1.0172853 1.448172
wall wall 1.037372 0.9447910 1.139026
> print(dnds_recurrent$globaldnds)
     name       mle     cilow    cihigh
wmis wmis 0.8320512 0.7686599 0.9006703
wnon wnon 0.7959551 0.6419031 0.9869784
wspl wspl 0.7436637 0.5797329 0.9539493
wtru wtru 0.7731282 0.6533462 0.9148706
wall wall 0.8271733 0.7650227 0.8943729

WXS only - by fraction

> print(dnds_shared$globaldnds)
     name      mle    cilow   cihigh
wmis wmis 1.165645 1.089492 1.247122
wnon wnon 1.193312 1.014441 1.403722
wspl wspl 1.289375 1.037991 1.601641
wtru wtru 1.225245 1.070728 1.402060
wall wall 1.169635 1.094162 1.250313
> print(dnds_primary$globaldnds)
     name      mle    cilow   cihigh
wmis wmis 1.079420 1.019339 1.143042
wnon wnon 1.165298 1.021122 1.329832
wspl wspl 1.258625 1.048818 1.510402
wtru wtru 1.194766 1.069075 1.335235
wall wall 1.088296 1.028528 1.151538
> print(dnds_recurrent$globaldnds)
     name      mle     cilow   cihigh
wmis wmis 1.046673 0.9918610 1.104515
wnon wnon 1.093988 0.9587044 1.248361
wspl wspl 1.151751 0.9763683 1.358636
wtru wtru 1.115333 1.0019560 1.241540
wall wall 1.051725 0.9973249 1.109093
fpbarthel commented 5 years ago

See also https://github.com/im3sanger/dndscv/issues/20

fpbarthel commented 5 years ago

Needs to be re-evaluated