MetaPhlAn version 4.0.6 (1 Mar 2023):
–Describe the issue
I tried to use calcaulate_diversity.R for alpha and beta diversity. I have some issue with command line from tutorials.
When I ran metaphlan4, I had only two txt files: 1) bowtie2.txt and 2) profile.txt.
In the tutorial, however, tsv file is used. My question is how I can produce tsv file from metaphlan run.
Another question is when I used profile.txt file for calculate_diversity.R, I got the following errors.
Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
Line starting ' install.packages → available.packages → readRDS
In addition: Warning message:
package âoptparseâ is not available (for R version 3.5.1)
Would someone please let me know how to calculate alpha and beta diversity from output of metaphlan?