Entering edit mode
3.5 years ago
ks.sholohova
▴
30
Hello everyone! My name is Kseniia and I am new here!
I did encounter some problems while analyzing american gut data. Here is the code for it:
library(devtools)
devtools::install_github("zdk123/SpiecEasi")
library(SpiecEasi)
SpiecEasi.matrix <- spiec.easi(amgut1.filt,
method = 'glasso',
lambda.min.ratio = 1e-2,
nlambda = 20,
icov.select.params=list(rep.num=50))
The next line suppose to add OTU names to rows and columns
rownames(SpiecEasi.matrix$refit) <- colnames(amgut1.filt)
Then this error appeared:
Error in rownames<-
(*tmp*
, value = c("OTU_1", "OTU_2", "OTU_3", "OTU_4", : attempt to set 'rownames' on an object with no dimensions
I understood that it appears because $refit is a list. But I don't know how to fix it. If anyone had the same error, I would greatly appreciate your help with its solution.
Thanks in advance! Kseniia
Thank you very much, Andres! Now everything perfectly works.
I just want to make sure please that I understand the concept, if you don't mind. So, SpiecEasi.matrix$refit is a list. That's why I got this error. Then by using SpiecEasi.matrix$refit$stars I refer to numeric object that is dimensional already and, hence, it works.
Have a nice day!
If this resolved your issue accept as answer - tick.