About mp_rrarefy and mp_cal_rarecurve
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- r
- Domain
- data, performance
Research direction
Start by reproducing the supplied R workflow with treated_array.txt and adjmeta.txt, focusing on mp_rrarefy() and mp_cal_rarecurve(). Trace which operation dominates runtime and review the resulting object sizes and parameters. Done means the slowdown is explained and a validated fix or clear usage guidance is provided.
Written by the indexing model from the issue text.
Description
Hi, I want to analyze the results of metaphlan using MicrobiotaProcess, below is my code：
mpse2 <- mp_import_metaphlan(profile='metaphlan/treated_array.txt', mapfilename='metaphlan/adjmeta.txt')
mpse2
mpse2 %<>% mp_rrarefy()
mpse2 %<>% mp_cal_rarecurve(.abundance = RareAbundance,chunks = 400)
Treated_array.txt is a merged metaphlan result. I converted the relative abundance to absolute abundance according to the number of reads.
[treated_array.txt](https://
adjmeta.txt
github.com/YuLab-SMU/MicrobiotaProcess/files/11269250/treated_array.txt)
I found that the calculation of mp_rrarefy and mp_cal_rarecurve is very slow, mp_rrarefy took me about half an hour, as for mp_cal_rarecurve I waited for two hours and still didn't get the result (so I terminated the program). I don't quite understand why it's taking so much time, and how can I fix it?
Thanks,
LeeLee
- Dominant language
- R
- Stars
- 196
- Forks
- 36
- PR merge metrics
- No merged PRs in 30d
Getting set up
This project ships no dev container, Dockerfile or contributing guide, so setting up is up to you: start from its README, and see our first-contribution guide for the general steps.
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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