missing-data {QFeatures} | R Documentation

## Managing missing data

### Description

This manual page describes the handling of missing values in QFeatures objects. In the following functions, if `object` is of class `QFeatures`, and optional assay index or name `i` can be specified to define the assay (by name of index) on which to operate.

The following functions are currently available:

- `zeroIsNA(object, i)` replaces all 0 in `object` by `NA`. This is often necessary when third-party software assume that features that weren't quantified should be assigned an intensity of 0.

- `infIsNA(object, i)` replaces all infinite values in `object` by `NA`. This is necessary when third-party software divide expression data by zero values, for instance during custom normalization.

- `nNA(object, i)` return a list of missing value summaries. The first element `nNA` gives a `DataFrame` with the number and the percentage of missing values for the whole assay; the second element `nNArows` provides a `DataFrame` of the number and the percentage of missing values for the features (rows) of the assay(s); the third element `nNAcols` provides the number and the percentage of missing values in each sample of the assay(s). When `object` has class `QFeatures` and additional column with the assays is provided in each element's `DataFrame`.

- `filterNA(object, pNA, i)` removes features (rows) that contain `pNA` percentage or more missing values.

See the Processing vignette for examples.

### Usage

    ## S4 method for signature 'SummarizedExperiment,missing'
    zeroIsNA(object, i)

    ## S4 method for signature 'QFeatures,integer'
    zeroIsNA(object, i)

    ## S4 method for signature 'QFeatures,numeric'
    zeroIsNA(object, i)

    ## S4 method for signature 'QFeatures,character'
    zeroIsNA(object, i)

    ## S4 method for signature 'SummarizedExperiment,missing'
    infIsNA(object, i)

    ## S4 method for signature 'QFeatures,integer'
    infIsNA(object, i)

    ## S4 method for signature 'QFeatures,numeric'
    infIsNA(object, i)

    ## S4 method for signature 'QFeatures,character'
    infIsNA(object, i)

    ## S4 method for signature 'SummarizedExperiment,missing'
    nNA(object, i)

    ## S4 method for signature 'QFeatures,integer'
    nNA(object, i)

    ## S4 method for signature 'QFeatures,numeric'
    nNA(object, i)

    ## S4 method for signature 'QFeatures,character'
    nNA(object, i)

    ## S4 method for signature 'SummarizedExperiment'
    filterNA(object, pNA = 0)

    ## S4 method for signature 'QFeatures'
    filterNA(object, pNA = 0, i)

### Arguments

`object` | An object of class `QFeatures` or `SummarizedExperiment`.
`i` | One or more indices or names of the assay(s) to be processed.
`pNA` | `numeric(1)` providing the maximim percentage of missing values per feature (row) that is acceptable. Feature with higher percentages are removed. If 0 (default), features that contain any number of `NA` values are dropped.

### Value

An instance of the same class as `object`.

### See Also

The `impute()` for `QFeautres` instances.

### Examples

    se_na2

    ## Summary if missing values
    nNA(ft_na, 1)

    ## Remove rows with missing values
    assay(filterNA(ft_na, i = 1))

    ## Replace NAs by zero and back
    ft_na <- impute(ft_na, i = 1, method = "zero")
    assay(ft_na)
    ft_na <- zeroIsNA(ft_na, 1)
    assay(ft_na)

[Package QFeatures version 1.2.0 Index]