How to add rowLinks, rowTree in SummarizedExperiment manually.
1
0
Entering edit mode
Muhammad • 0
@0ddee349
Last seen 8 days ago
Belgium

Hello,

I am really sorry if it's not the kind of question I should be asking here but I did not find any help at BioStars forum, so...

I am trying to incorporate my "taxonomy table" from metagenomic reads data into Tree/SummarizedExperiment and have found no luck. The tutorials/workflow I have seen are using "Global Patterns" dataset which does not require importing rowLinks, rowTree data manually.

My code:

counts <- read.csv("counts_file.csv", header = T)
pdata <- read_csv("coldata_file.csv")
taxa <- read.csv("taxa_file.csv")    
pdata <- column_to_rownames(pdata, "sample_id")    
counts <- column_to_rownames(counts, "species")    
se <- SummarizedExperiment(t(counts), colData = pdata, rowData = taxa)    
se
tse <- as(se, "TreeSummarizedExperiment")
tse

this is how my tse looks like:

class: TreeSummarizedExperiment 
dim: 3107 27 
metadata(0):
assays(1): ''
rownames(3107): X.Candida._auris X.Candida._duobushaemulonis ... Zymomonas_mobilis
  Zymoseptoria_tritici
rowData names(7): domain phylum ... genus species
colnames(27): control_2 ILVO650SCE ... ILVO747CE winter78Healthy
colData names(3): health_status group sample_location
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
rowLinks: NULL
rowTree: NULL
colLinks: NULL
colTree: NULL

I know I cannot just make tse with as function but I have not found an alternative way to fix this.

Thanks for your help.

TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment • 63 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States

Does the vignette not help?

Login before adding your answer.

Traffic: 370 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6