Error input data must be numeric in R, how to solve it?

Question

[Amr]

Error input data must be numeric, how to solve it?

I am trying to perform Alpha diversity for microbiome analysis in R, I got an error when ASV file is the input data although it has numeric values:

Error in diversity(ASV, index = "shannon") : input data must be numeric

[Dunois]

What is the package you're trying to use here? What does your data look like? It is an Excel file? Is it a CSV file? Or has this "ASV" data been loaded into the environment already?

[Amr]

The data is text file (I opened it as csv to show you) and it looks like that

Answer 1

[Gordon Smyth]

I am guessing you are using microbiome::diversity function in the Bioconductor microbiome package. The help page for the function says:

Usage

diversity(x, index = "all", zeroes = TRUE)

Arguments

• x A species abundance vector, or matrix (taxa/features x samples) with the absolute count data (no relative abundances), or phyloseq-class object
• index Diversity index. See details for options.
• zeroes Include zero counts in the diversity estimation.

So it is clear that you need to give the function a numeric vector or matrix, not a data.frame or csv file.

[Amr]

Thanks for your answer, so x is the taxa file?

[Gordon Smyth]

Please read the help again. x is a vector or a matrix, not a file. You have to create the matrix from the file, for example by:

x <- read.csv("taxa.csv", row.names=1)

[Amr]

Thanks a lot