Can't recognize input data in setting up

Hello, I’ve been trying to start using Maaslin2, running the program through R(ver. 3.6.3).
I use macOS Catalina(ver.10.15.7).

After installing package “Maaslin2” by Bioconducter, I’ve been trying to run the protocol according to tutorial. (MaAsLin2 · biobakery/biobakery Wiki · GitHub)

I created new directory named “R_Maaslin_tutorial” on Desktop, of course.

Then, I downloaded the two kinds of files from the “inst/extdata” folder of the “MaAsLin 2” source, which are taxonomy and metadata.

On chapter [3.1 “MaAsLin 2” Input] in tutorial, I tried to write scripts below for setting up:

input_data = system.file(“extdata”, “HMP2_taxonomy.tsv”, package=“Maaslin2”) # The abundance table file

input_metadata = system.file(“extdata”, “HMP2_metadata.tsv”, package=“Maaslin2”) # The metadata table file

specifically, I wrote

input_data = system.file(“extdata”, “~Desktop/R_Maaslin_tutorial/Sample_MaAsLin2_tutorial_taxonomy2.tsv”, package=“Maaslin2”)

and then, I also wrote

for confirming the file (~Desktop/R_Maaslin_tutorial/Sample_MaAsLin2_tutorial_taxonomy2.tsv) was set up as input_data, but there was a message in R console below;
[1] “”

Does it means there wasn’t any kinds of files for input_data?

I also tried to write the command below as the tutorial says;

df_input_data = read.table(file = input_data, header = TRUE, sep = “\t”, row.names = 1, stringsAsFactors = FALSE)

but there was a error message below;
read.table(file = input_data, header = TRUE, sep = “\t”, row.names = 1, でエラー:
入力中には利用可能な行がありません(No lines available during input)

I think I failed to complete for setting up the taxonomy data downloaded from tutorial(~Desktop/R_Maaslin_tutorial/Sample_MaAsLin2_tutorial_taxonomy2.tsv) .

This is my first work for using R, so my question might be so amateur, sorry.

Could you tell me if you have any good solution for this problem? I have no idea what I should do next…

and the Taxonomy data and Matedata file as follow
Sample_MaAsLin2_tutorial_metadata2.tsv (96.9 KB)
Sample_MaAsLin2_tutorial_taxonomy2.tsv (772.0 KB)

Best regards.

If you’ve installed Maaslin2 correctly and are just trying to run the tutorial, you shouldn’t need to change these commands. The system.file() function should find the right path on your system to the data inside the directory where Maaslin2 is installed. For example on my Windows machine the first command yields "C:/Users/aghazi/AppData/Local/R/win-library/4.2/Maaslin2/extdata/HMP2_taxonomy.tsv"