Question: Decontam data import (phyloseq?)
0
gravatar for goliat0704
4 months ago by
goliat07040
goliat07040 wrote:

I'm new to R and have trouble importing data to decontam as phyloseq objects. The OTU table and taxonomy is in .txt and the metadata in an excel file. Could someone help?

R • 331 views
ADD COMMENTlink modified 3 months ago by plicht0 • written 4 months ago by goliat07040

Hi,

Can you provide the code that you used or the error that you got, please?

António

ADD REPLYlink written 4 months ago by antonioggsousa1.5k

Hey Antonio,

I am alsy new to are and have troubles importing the MetaPhlAn3 output table as a phyloseq object to use that for the R package decontam. I merged several metaphlan analyses with the metaphlan internal command "merge_table".

Then I imported the data into R using the read.table command:

merged_metaphlan <- read.table("/media/sf_projects/microbiome/Analysis_of_microbiome/WiP/KneadData/firsttry/Validation_Samples_PL018/PL0183103_5/subsamples/visualization/merged_subsamples_samples_1,2,5.txt", header = TRUE)

After that, I wanted to assign this to an otu_table

otu_table(merged_metaphlan, taxa_are_rows = TRUE)

and I receive:

Error in validObject(.Object) : invalid class “otu_table” object: 
 Non-numeric matrix provided as OTU table.
Abundance is expected to be numeric.

What am I doing wrong?

ADD REPLYlink modified 3 months ago by genomax92k • written 3 months ago by plicht0

Hi,

Your data merged_metaphlan contains columns that are character or factor, i.e., not all the columns are numbers.

Can you provide a quick overview of the table here, by doing:

head(merged_metaphlan)

Though I would advise you to add a new post with this issue, because it is not related with the question on this post.

António

ADD REPLYlink modified 3 months ago • written 3 months ago by antonioggsousa1.5k

Thanks a lot for the prompt answer! Here is an overview of the object merged_metaphlan

> head(merged_metaphlan)
                                                                                  clade_name              NCBI_tax_id          X1          X2       X5 1 UNKNOWN                       -1 53.48292000 63.13894000  0.00000 2    k__Bacteria                        2 44.73274078 36.56062797 99.81208 3                                                              k__Bacteria|p__Actinobacteria                 2|201174 38.79252825
32.01578501  0.00000 4                                            k__Bacteria|p__Actinobacteria|c__Actinobacteria            2|201174|1760 38.79252825 32.01578501  0.00000

If i can't use characters, do I need to abbreviate the clade name with numbers and link the real clade name to the numbers in another file? Or is there another possibility of a work around?

Either way, I will also post this as a new issue :)

ADD REPLYlink modified 3 months ago by genomax92k • written 3 months ago by plicht0
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