filter_samples_by_mv {pmp} | R Documentation

## Filter samples by missing values

### Description

Missing values in mass spectrometry metabolomic datasets occur widely and can originate from a number of sources, including for both technical and biological reasons. In order for robust conclusions to be drawn from down-stream statistical testing procedures, the issue of missing values must first be addressed. This tool facilitates the removal of samples containing a user-defined maximum percentage of missing values.

### Usage

    filter_samples_by_mv(df, max_perc_mv, classes = NULL, remove_samples = TRUE)

### Arguments

`df` | A matrix-like (e.g. an ordinary matrix, a data frame) or RangedSummarizedExperiment-class object with all values of class `numeric()` or `integer()` of peak intensities, areas or other quantitative characteristic.
`max_perc_mv` | `numeric(1)`, Value between 0 and 1 of threshold of missing value percentage in sample.
`classes` | `character()`, vector of class labels. Must be the same length as the number of sample in the input peak table. If input is `SummarizedExperiment` object, use `SummarizedExperiment_object$meta_data_column_name`.
`remove_samples` | `logical(1)`, remove blank samples from peak matrix or not.

### Value

Object of class `SummarizedExperiment`. If input data are a matrix-like (e.g. an ordinary matrix, a data frame) object, function returns `numeric()` matrix-like object of filtered data set. Function `flags` are added to the object `attributes` and is a DataFrame-class with five columns. The same `DataFrame` object containing flags is added to `rowData()` element of `SummarizedExperiment` object as well. If element `colData()` already exists flags are appended to existing values.

Columns in `colData()` or `flags` element contain:
`perc_mv` `numeric()`, fraction of missing values per sample;
`flags` `integer()`,if 0 feature is flagged to be removed.

### Examples

    df <- MTBLS79
    out <- filter_samples_by_mv (df=df, max_perc_mv=0.8)

[Package pmp version 1.2.1 Index]