Compute prevalence and abundance summary of each species/OTU for different variables

[apoosakkannu]

Hi, i wonder could it be possible to get prevalence and abundance summary of all the otus in a object somthing like mentioned in https://rdrr.io/github/vmikk/metagMisc/src/R/prevalence.R, but prevalence and abundance for different variables taken into consideration. please let me know if it is possible.

Your help is very much appreciated so far shaping up my manuscript.

[ChiLiubio]

Hi. To temporarily get such result, please use file2meco package to convert your microtable data.

library(microeco)
library(file2meco)
library(phyloseq)
data("dataset")
# load https://rdrr.io/github/vmikk/metagMisc/src/R/prevalence.R
test <- prevalence(meco2phyloseq(dataset))

[apoosakkannu]

Thanks, I could do that. Just want to get extra than that to get prevalence based on a factor. I mean to get abundance and prevalence for each sample and/or a factor.

[ChiLiubio]

It is ok to write a simple for cycle to do that if the group number is large.

[apoosakkannu]

I am not much familiar with for cycle. I tried and it did not work. Could you please give me some toy example? Thanks in advance!

[ChiLiubio]

Hi. This is a simple example.

library(microeco)
library(file2meco)
library(magrittr)
library(phyloseq)
data("dataset")
# load https://rdrr.io/github/vmikk/metagMisc/src/R/prevalence.R
allgroups <- unique(dataset$sample_table[, "Group"])
allresult <- data.frame()
for(i in allgroups){
	tmp <- clone(dataset)
	tmp$sample_table %<>% .[.$Group == i, ]
	tmp$tidy_dataset()
	tmp_res <- prevalence(meco2phyloseq(tmp))
	tmp_res <- data.frame(Feature = rownames(tmp_res), tmp_res, Group = i)
	allresult <- rbind(allresult, tmp_res)
}
View(allresult)