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_data
input_metadata = system.file(“extdata”, “HMP2_metadata.tsv”, package=“Maaslin2”) # The metadata table file
input_metadata
specifically, I wrote
input_data = system.file(“extdata”, “~Desktop/R_Maaslin_tutorial/Sample_MaAsLin2_tutorial_taxonomy2.tsv”, package=“Maaslin2”)
and then, I also wrote
input_data
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.