filter_peaks_by_rsd {pmp} | R Documentation

## Filter features by RSD% of QC samples

### Description

Metabolomics datasets often contain 'features' with irreproducible peak intensity values, or with large numbers of missing values. This tool facilitates the remove of such features from a data matrix, based upon relative standard deviation of intensity values for a given feature within specified QC samples.

### Usage

    filter_peaks_by_rsd(df, max_rsd, classes, qc_label, remove_peaks = 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_rsd` | `numeric()`, threshold of QC RSD% value
`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`.
`qc_label` | `character(1)` or `NULL`, class label used to identify QC samples.
`remove_peaks` | `logical(1)`, remove filtered features 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-class` object containing flags is added to `rowData()` element of `SummarizedExperiment` object as well.
Columns in `rowData()` or `flags` element contain:
`rsd_QC` `numeric()`, RSD% value of QC samples per feature;
`rsd_flags` `integer()`,if 0 feature is flagged to be removed.

### Examples

    df <- MTBLS79[ ,MTBLS79$Batch == 1]
    out <- filter_peaks_by_rsd(df=df, max_rsd=20,
        classes=df$Class, qc_label='QC')

[Package pmp version 1.0.0 Index]