summarize.features.Rd
This function summarize features on a specific taxonomic level
summarize.features(siamcat, level = 'g__', feature.type='original', verbose=1)
siamcat | object of class siamcat-class |
---|---|
level | string, at which level to summarize (e.g. |
feature.type | string, on which type of features should the function
work? Can be either |
verbose | integer, control output: |
object of class siamcat-class with a summarized feature table
This function will summarize features at different taxonomic levels, e.g. transform species-level relative abundance into genus-level taxonomic profiles.
The function expects feature names which encode taxonomic information, e.g.
k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Acidimicrobiales;..
Then, for a given taxonomic level (e.g. g__
), the function will
sum up all the relative abundances of features belonging to the same group
at that specific taxonomic level.
Please note that this function is currently maturing and not necessarily reliable!!!
## load the phyloseq example data data("GlobalPatterns") feat <- otu_table(GlobalPatterns)[1:500,] label <- create.label(meta=sample_data(GlobalPatterns), label = "SampleType", case = c("Freshwater", "Freshwater (creek)", "Ocean"))#>#> #> #>#># rename features to create feature names containing taxonomic information temp <- tax_table(GlobalPatterns)[1:500,] test <- apply(temp, 1, FUN=function(vec){ out <- '' for (i in seq_along(vec)){ end <- ifelse(i == ncol(temp), '', ';') x <- colnames(temp)[i] x2 <- tolower(substr(x, 1, 1)) out <- paste0(out, x2, '__', vec[i], end) } return(out)}) rownames(feat) <- test # run the constructor function siamcat <- siamcat(feat=feat, label=label, verbose=1)#> Warning: ### Warning: The data do not seem to consist of relative abundances!#>#>#>siamcat <- summarize.features(siamcat, level='g__', verbose=3)#>#>#>#>