Unuploaded R script in FMT_select_validation_predition

[Axolotl233]

Hi,

Recently I read this paper and it is an excellent work that inspired me. But when i read the code, the script pre_FMT_sel.R used in FMT_select_validation_predition step can not be found anywhere in this repository. Could you kindly provide it? i will very be appreciated it.

Thanks,
Nemo

[RuiqiaoHe]

Hi Nemo,

Thank you for your appreciation. We have uploaded pre_FMT_sel.R in the folder analysis_code_Rmd. Hope this will meet your needs.

Best,
RuiqiaoHe

[Axolotl233]

thank you for quickly reply. it perfect ! i will download it right now

[Axolotl233]

Hi Ruiqiao,

Sorry for bothering you again, I have tested part of the script, and it worked. But other parts lack input tables of "ma_arare" and "fmt_meta.txt". Could you kindly provide it again?

I am a new Ph.D. candidate in microbiology, so my progress is a bit slow. I will be very grateful to me if you give me any help.

Best,
Nemo

[RuiqiaoHe]

Hi Nemo,

I am happy to hear that our model script works for you. The two input tables are the alpha diversity file ("ma_arare") and the FMT relationship file ("fmt_meta.txt"). Their format will be described below, and you can change it according to your own project:

• ma_arare:

--	shannon	chao1	observed_otus
Sample 1	--	--	--
Sample 2	--	--	--
...	--	--	--
Sample N	--	--	--

• fmt_meta.txt:

SRA_Sample	Status	Time	ID	PRJ	Sex	Age	Diease1	postfmt_symptoms	Donor_sra	Previous_sra
Sample 1	--	--	--	--	--	--	--	--	--	--
Sample 2	--	--	--	--	--	--	--	--	--	--
...	--	--	--	--	--	--	--	--	--	--
Sample N	--	--	--	--	--	--	--	--	--	--

Hope this information can help you!