countUniqueFeatures {QFeatures} | R Documentation

## Count Unique Features This function counts the number of unique features per sample. A grouping structure can be provided to count higher level features from assays, for example counting the number of unique proteins from PSM data.

### Description

Count Unique Features

This function counts the number of unique features per sample. A grouping structure can be provided to count higher level features from assays, for example counting the number of unique proteins from PSM data.

### Usage

    countUniqueFeatures(object, i, groupBy = NULL, colDataName = "count")

### Arguments

`object` | An object of class `QFeatures`.
`i` | A `numeric()` or `character()` vector indicating from which assays the `rowData` should be taken.
`groupBy` | A `character(1)` indicating the variable name in the `rowData` that contains the grouping variable, for instance to count the unique number of peptides or proteins expressed in each samples (column). If `groupBy` is missing, the number of non zero elements per sample will be stored.
`colDataName` | A `character(1)` giving the name of the new variable in the `colData` where the number of unique features will be stored. The name cannot already exist in the `colData`.

### Value

An object of class `QFeatures`.

### Examples

    data("ft_na")
    ## Count number of (non-missing) PSMs
    ft_na <- countUniqueFeatures(ft_na,
                                 i = "na",
                                 colDataName = "counts")
    ft_na$counts
    ## Count number of unique rowData feature
    ft_na <- countUniqueFeatures(ft_na,
                                 i = "na",
                                 groupBy = "Y",
                                 colDataName = "Y_counts")
    ft_na$Y_counts

[Package QFeatures version 1.2.0 Index]