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

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

error_numeric asv_file r
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written by Amr • Amr

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?

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written by Dunois • Dunois

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

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written by Amr • Amr

1 answer

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.

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written by Gordon Smyth Gordon Smyth

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

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written by Amr • Amr

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)
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written by Gordon Smyth Gordon Smyth

Thanks a lot

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written by Amr • Amr

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