summarize.features {SIAMCAT}R Documentation

Summarize features

Description

Summarize features

Usage

summarize.features(siamcat, level = 'g__',
    keep.original.names=TRUE, feature.type='original',
    verbose=1)

Arguments

siamcat

object of class siamcat-class

level

at which level to summarize (g__ = genus)

keep.original.names

boolean, should the original names be kept?

feature.type

On which type of features should the function work? Can be either "original", "filtered", or "normalized". Please only change this paramter if you know what you are doing!

verbose

control output: 0 for no output at all, 1 for only information about progress and success, 2 for normal level of information and 3 for full debug information, defaults to 1

Value

object of class siamcat-class with a summarized feature table

Examples


data("GlobalPatterns") ## phyloseq example data
feat <- otu_table(GlobalPatterns)[1:500,]
label <- create.label(meta=sample_data(GlobalPatterns),
    label = "SampleType",
    case = c("Freshwater",
        "Freshwater (creek)",
        "Ocean"))
# rename features
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)
siamcat <- summarize.features(siamcat, level='g__', verbose=3)
[Package SIAMCAT version 1.2.1 Index]