Question: bug in nem's transitive.reduction? (and thus rBiopaxParser)
gravatar for Ramon Diaz-Uriarte
2.7 years ago by
Ramon Diaz-Uriarte70 wrote:

transitive.reduction in nem does not always return the transitive reduction unless one applies transitive.reduction on the transitive closure of the graph. So I think that either the code should be fixed (by using transitive.closure first) or the documentation fixed (but this second route seems dangerous for those who do not read the help carefully).  This bug will probably also affect rBiopaxParser (its transitiveReduction function).


Examples below taken from discussion and comments in  as well as comments to

m1 <- matrix(0, nrow = 4, ncol = 4)
colnames(m1) <- rownames(m1) <- LETTERS[1:4]
m1[rbind(c(1, 2),
         c(2, 3),
         c(3, 4),
         c(1, 4))] <- 1

## Wrong, since A connected to D directly and through B-> C
## OK

m2 <- matrix(0, nrow = 4, ncol = 4)
colnames(m2) <- rownames(m2) <- LETTERS[1:4]
m2[rbind(c(1, 2),
         c(2, 3),
         c(3, 4),
         c(1, 3),
         c(1, 4))] <- 1

## Wrong, since A connected to D directly and through B-> C
## OK


nem rbiopaxparser graphs • 423 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Ramon Diaz-Uriarte70

Dear Ramon,

as you noticed rBiopaxParser uses the transitive reduction function implemented in package nem.

Holger Fröhlich (package maintainer)  mentioned that a bug fix for this should be supplied with the next nem version.


Best wishes,

ADD REPLYlink written 2.7 years ago by Frank Kramer60
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