subsetSamples {mia} | R Documentation

## Subset functions

### Description

To make a transition from `phyloseq` easier, the `subsetSamples` and `subsetFeatures` functions are implemented. To avoid name clashes they are named differently.

### Usage

    subsetSamples(x, ...)

    subsetFeatures(x, ...)

    subsetTaxa(x, ...)

    ## S4 method for signature 'SummarizedExperiment'
    subsetSamples(x, ...)

    ## S4 method for signature 'SummarizedExperiment'
    subsetFeatures(x, ...)

    ## S4 method for signature 'SummarizedExperiment'
    subsetTaxa(x, ...)

### Arguments

`x` | a `SummarizedExperiment` object
`...` | See `subset`. `drop` is not supported.

### Details

However, the use of these functions is discouraged since subsetting using `[` works on both dimension at the same time, is more flexible and is used throughout R to subset data with two or more dimension. Therefore, these functions will be removed in Bioconductor release 3.15 (April, 2022).

### Value

A subset of `x`

### Examples

    data(GlobalPatterns)
    subsetSamples(GlobalPatterns, colData(GlobalPatterns)$SampleType == "Soil")
    # Vector that is used to specify subset must not include NAs
    subsetFeatures(GlobalPatterns, rowData(GlobalPatterns)$Phylum == "Actinobacteria" &
                   !is.na(rowData(GlobalPatterns)$Phylum))

[Package mia version 1.2.7 Index]