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bradfordcondon / WGPAN

Whole-Genome Pairwise Alignment Noising
http://www.bradfordcondon.com
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withinDistanceTable has NA for third column #17

Closed bradfordcondon closed 5 years ago

bradfordcondon commented 5 years ago

from vignette:

WithinDistanceTable <- withinGroupDistances(distanceMatrix = x, cladeAssignments = cladeAssignments, ID_names = ID_names)

head(WithinDistanceTable)
  distance      clade       NA
1     9399 Agaricales  Amanita
2     4973 Agaricales  Amanita
3     5883 Agaricales Coprinus
4     4473 Agaricales Coprinus
5     3377 Agaricales Entoloma
6     1699 Agaricales Entoloma

breaks the vignette.

bradfordcondon commented 5 years ago

colnames(allSelfDists) <- c("distance", "clade") should be colnames(allSelfDists) <- c("distance", "clade", "ID")

bradfordcondon commented 5 years ago

actually whats the deal with this third column? Should it actually be 4 columns, with column 3 = partner 1 and 4 = partner 2? need to look mroe carefully at what hte function does

 WithinDistanceTable
  distance       clade         ID
1     1894  Agaricales    Amanita
2     9923  Agaricales    Amanita
3     3622  Agaricales   Coprinus
4     1561  Agaricales   Coprinus
5     9920  Agaricales   Entoloma
6     9864  Agaricales   Entoloma
7     1282 Polyporales  Polyporus
8     6350 Polyporales Flaviporus
9     6350 Polyporales Flaviporus

edit:

OK so its intentional. we could add the partner column but maybe not necessary. It's saying Distance to otehr clade members, for that participant.

Xylaria is missing because there are no partners, so thats as intended.