Closed fpbarthel closed 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
See also https://github.com/im3sanger/dndscv/issues/20
Needs to be re-evaluated
Noticed that there was a significant WGS - WXS discrepancy in dNdS values:
WGS only - all
WXS only - all
However, after running each separately by fraction, the results are similar to the overall results.
WGS only - by fraction
WXS only - by fraction