Open Fla1487 opened 5 years ago
@Fla1487 this isn't really a phyloseq question, but the problem appears to be that you are missing the data.table
function. Have you loaded this (e.g. library(data.table)
) ?
Thank you so much, I have then charged the indicated package. Below the command and the output in R:
lefse.tbl <- lefse(phy_obj1,class="Type", levels = "Genus") [1] "Wrote lefse.res" Error in file(file, "rt") : cannot open the connection In addition: Warning messages: 1: Column
sample
joining factor and character vector, coercing into character vector 2: In file(file, "rt") : cannot open file 'lefse.res': No such file or directory
As output I obtain a txt file, that I can use on Galaxy LEFSE. I have checked this file, but it does not have the suggested format.
is it the result of R LEFSE function? or Can I have obtain the plot in R?
Thank you again
Moreover, I have tried with the lefse2 (modified according to https://github.com/ying14/yingtools2/wiki/Using-the-%60lefse%60-wrapper-function)
Below the result:
lefse.tbl <- lefse2(phy_obj1, class="Type", subclass = "Hurleyscore") Error in gsub(" ", "", taxon) : object 'taxon' not found Called from: gsub(" ", "_", taxon)
Thank you so much
Again, not sure if this specific venue (issue tracker for phyloseq) is the appropriate place to ask this? The yingtools2 repo tracker seems more appropriate.
how can I change the section? I think that this trouble impacts also on phyloseq (it uses a phyloseq object)
how do you explain these problems?
Hi @Fla1487
Did you solve this problem? Or did you move the question to another section?
I have the same error message in the lefse2 function and I don't know how to solve it.
Thank you!!
how can I change the section? I think that this trouble impacts also on phyloseq (it uses a phyloseq object)
how do you explain these problems?
Unfortunatly, I do not solve this problem. R and Lefse analysis do not work on windows. I have even tried on ubuntu, but I did not obtain any result. To perform Lefse, I have used the online softare microbiome analyst, I will prefer doing anything in R.
@Fla1487 have you asked @ying14 about this (issue in the above repo)? It's more direct.
no I didn't I tried both lefse and lefse 2. I tried unsuccesfully to upload the txt file on galaxy.
@Fla1487
I have oppened an issue in the yingtools2 repo:
Maybe you can try my package: microbial. It's on CRAN now. Kai
Maybe you can try my package: microbial. It's on CRAN now. Kai
Thank you so much, I will try your package
Maybe you can try my package: microbial. It's on CRAN now. Kai
Maybe, the package is not released for R in windows or it does not work in R > 4.0???
Please try to use devtools::install_github(‘guokai8/microbial’). And it should work. Best, Kai
Please try to use devtools::install_github(‘guokai8/microbial’). And it should work. Best, Kai
Thank you so much...now it works... I will try your package on a new dataset...
Dear All,
I have a bit problem with the LESFE analysis starting from a phyloseq object.
I tried to use the LEFSE package from ying14/yingtools2: Ying's R Tools, following the exemple code. Below you will find the command and the result:
lefse.tbl <- lefse(phy_obj1,class="Type") Error in data.table(otutab, keep.rownames = TRUE) : could not find function "data.table"
I do not understand the problem.
Additionally, I would like perform LEFSE analysis on galaxy, how can I obtain th txt file to upload? is it a good idea?
Thank you in advance.