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.
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
as function but I have not found an alternative way to fix this.
Thanks for your help.