Entering edit mode
2.3 years ago
Muhammad
•
0
Hello,
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.
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.
You can post your question on the github issues page of TreeSummarizedExperiment: (https://github.com/markrobinsonuzh/TreeSummarizedExperiment/issues)