I'm trying to get the coefficients of the taxa that generate the most differences between the groups in my permutest of types of supplies for the animals. I paste the results of the permutest:
permutest(betadispersionAlimentación, pairwise = TRUE) enter image description here
When I try to get the coefficients, Studio answer me with this:
coefficients(betadispersionAlimentación)["C",] NULL
The object to get the coefficients is the type of: Permanova? Betadisper? Permutest?
i don't know how can I get the taxa (genus, Family, Specie...) that contribute to the differences.
can anybody help me, please?
Thanks a lot!
For anybody who have the same problem. From the day that I posted the question I have worked about that. To get de genus or the specie that more contribute to the dissimilarity I used the vegan library.
Here I used the Vegan Distance to create de distance object
DIST_ABUNDANCES <- vegdist(t(OTU_ABUNDANCES))
Here I took the anova function to create all the values.
anova(betadisper(DIST_ABUNDANCES, META_ABUNDANDES$Sexo))
Here I made the permutest to compare all the values of the variable Sexo
permutest(betadisper(DIST_ABUNDANCES, META_ABUNDANDES$Sexo), pairwise = TRUE)
Here I took the correlation coefficients of the anova to seek the objetive
COEF_ABUNDANCES <- coefficients(PERMANOVA_ABUNDANCES)["Sexo1",]
I created the top coeficients object
TOP.COEF_ABUNDANCES <- COEF_ABUNDANCES[rev(order(abs(COEF_ABUNDANCES)))[1:20]]
Here I designed the plot of the coefficients
par(mar = c(3, 14, 2, 1))
barplot(sort(TOP.COEF_ABUNDANCES), horiz = T, las = 1, main = "Top taxa")
I followed this tutorial: https://mibwurrepo.github.io/Microbial-bioinformatics-introductory-course-Material-2018/multivariate-comparisons-of-microbial-community-composition.html