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]