MetaCellFiltering {DAPAR} | R Documentation

## Filter lines in the matrix of intensities w.r.t. some criteria

### Description

Filters the lines of `exprs()` table with conditions on the number of missing values. The user chooses the minimum amount of intensities that is acceptable and the filter delete lines that do not respect this condition. The condition may be on the whole line or condition by condition.

### Usage

    MetaCellFiltering(obj, indices, cmd, processText = "")

### Arguments

`obj` | An object of class `MSnSet` containing quantitative data.
`indices` | A vector of integers which are the indices of lines to keep.
`cmd` | xxxx. Available values are: 'delete', 'keep'.
`processText` | A string to be included in the `MSnSet` object for log.

### Details

The different methods are : "WholeMatrix": given a threshold `th`, only the lines that contain at least `th` values are kept. "AllCond": given a threshold `th`, only the lines which contain at least `th` values for each of the conditions are kept. "AtLeastOneCond": given a threshold `th`, only the lines that contain at least `th` values, and for at least one condition, are kept.

### Value

An instance of class `MSnSet` that have been filtered.

### Author(s)

Florence Combes, Samuel Wieczorek

### Examples

    utils::data(Exp1_R25_pept, package='DAPARdata')
    obj <- Exp1_R25_pept[1:1000]
    level <- obj@experimentData@other$typeOfData
    metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
    indices <- GetIndices_WholeLine(metacell.mask)
    obj.filter <- MetaCellFiltering(obj, indices, 'delete')

[Package DAPAR version 1.24.8 Index]