getAbundance {mia} | R Documentation

## Get abundance values by “SampleID” or “FeatureID”

### Description

These are functions for extracting abundances present in `assay(x)`. These functions are convenience wrapper around subsetting columns or rows from `assay(x,name)`.

### Usage

    getAbundanceSample(x, sample_id, abund_values = "counts")

    ## S4 method for signature 'SummarizedExperiment'
    getAbundanceSample(x, sample_id = NULL, abund_values = "counts")

    getAbundanceFeature(x, feature_id, abund_values)

    ## S4 method for signature 'SummarizedExperiment'
    getAbundanceFeature(x, feature_id = NULL, abund_values = "counts")

### Arguments

`x` | A `SummarizedExperiment` object.
`sample_id` | A “SampleID” from which user wants to extract the abundances of “FeatureID”. This is essentially a column name in `assay(x)`.
`abund_values` | a `character` value to select an `assayNames`
`feature_id` | A “FeatureID” for which user wants to extract the abundances from all of “SampleID” in `assayNames`. This is essentially a rowname in `assay(x)`.

### Details

`getAbundanceSample` returns abundance values for all “FeatureIDs” in a user specified “SampleID”.

`getAbundanceFeature` returns abundance values in all “SampleIDs” for user specified “FeatureID”.

### Value

`getAbundanceSample` and `getAbundanceFeature` return a numeric matrix of the abundance values for all “SampleIDs”/“FeatureIDs”

### Author(s)

Sudarshan A. Shetty

### Examples

    # getAbundanceSample
    data(GlobalPatterns)
    getAbundanceSample(GlobalPatterns,
                       sample_id = 'CC1',
                       abund_values = 'counts')
    # getAbundanceFeature
    getAbundanceFeature(GlobalPatterns,
                        feature_id = '522457',
                        abund_values = 'counts')

[Package mia version 1.2.7 Index]