I want to calculate the distance matrix of a phylogenetic tree which is stored in R as a class “large phylo”. This tree have 23197 tips.
when I use cophenetic() to calculate the distance matrix, a error was given.
Error in double(nm * nm) : vector size cannot be NA In addition: Warning message: In nm * nm : NAs produced by integer overflow
But when I use a small phylogenetic tree to do this.
There’s no wrong!
Can any one tell me how can I fix this problem???
Thanks!
These are only guesses:
R tends to try to hold everything in memory at once. This works great up to a certain number of things (lengths of vectors generated, etc.) But, the size of a problem during the actual calculations may be a great deal larger than you think. You might consider leaving some features out if you can get by dropping them.
Another guess is that the problem could involve hclust() which I assume is used before cophenetic()
Good luck
Hello Maccarter,
Thank you for your kind help. The size of tree is actually the problem and I already solved this problem by discarding some rare OTUs and cophenetic() worked.
- Badges
- Science topic
- Similar topics
- Mathematics
- Statistics
- Statistical Software
- R Statistical Package