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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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How to merge the same data for analysis? #1713

Open lingvv opened 10 months ago

lingvv commented 10 months ago

For my case, I have a few duplicates for the same samples

For example:

Illeum_Dose1_Sample1
Illeum_Dose1_Sample2
Illeum_Dose1_Sample3

Illeum_Dose2_Sample1
Illeum_Dose2_Sample2
Illeum_Dose2_Sample3

Ceca_Dose1_Sample1
Ceca_Dose1_Sample2
Ceca_Dose1_Sample3

Ceca_Dose2_Sample1
Ceca_Dose2_Sample2
Ceca_Dose2_Sample3

My phyloseq object:

phyloseq-class experiment-level object 
otu_table()   OTU Table:         [ 1603 taxa and 48 samples ] 
sample_data() Sample Data:       [ 48 samples by 1 sample variables ] 
tax_table()   Taxonomy Table:    [ 1603 taxa by 6 taxonomic ranks ]

My metadata:

                                      type
Illeum_Dose1_Sample1      Illeum
Illeum_Dose1_Sample2      Illeum
Illeum_Dose1_Sample3      Illeum
Illeum_Dose2_Sample1      Illeum
Illeum_Dose2_Sample2      Illeum
Illeum_Dose2_Sample3      Illeum
Ceca_Dose1_Sample1        Ceca
Ceca_Dose1_Sample2        Ceca
Ceca_Dose1_Sample3        Ceca
Ceca_Dose2_Sample1        Ceca
Ceca_Dose2_Sample2        Ceca
Ceca_Dose2_Sample3        Ceca

Referring to the data above, may I kindly ask what should I do, to merge Illeum_Dose1_Sample1 Illeum_Dose1_Sample2 Illeum_Dose1_Sample3 into one for analysis purpose (the same for others)

I tried the tutorial from https://joey711.github.io/phyloseq/merge.html#merge_phyloseq But it doesn't work for me

It would be great if I could get some help for this Appreciate your time and help!

adossantos1 commented 10 months ago

The simplest way would probably be to add another column to your data like so: sample_data(phy)$type_dose <- sub("_Sample.*$","",sample_names(phy))

And then you can merge on the new column (type_dose): merge_samples(phy, "type_dose")