get_alltaxadf {MicrobiotaProcess} | R Documentation |
This function was designed to get the abundance of all level taxonomy, the input can be phyloseq object or data.frame.
get_alltaxadf(obj, ...) ## S4 method for signature 'phyloseq' get_alltaxadf(obj, method = NULL, type = "species", ...) ## S4 method for signature 'data.frame' get_alltaxadf( obj, taxda, taxa_are_rows = FALSE, method = NULL, type = "species", ... )
obj |
object, phyloseq or data.frame |
..., |
additional parameters, see also |
method |
character, the normalization method,
see also |
taxda |
data.frame, the taxonomy table. |
taxa_are_rows |
logical, if the obj is data.frame, and the features are rownames, the taxa_are_rows should be set TRUE, default FALSE, meaning the features are colnames. |
the all taxonomy abundance table
Shuangbin Xu
data(test_otu_data) alltaxatab <- get_alltaxadf(test_otu_data) head(alltaxatab[,1:10])