mvFilterGetIndices {DAPAR} | R Documentation

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

### Description

Returns the indices of the lines of `exprs()` table to delete w.r.t. the 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

    mvFilterGetIndices(
      obj,
      percent = FALSE,
      condition = "WholeMatrix",
      threshold = NULL
    )

### Arguments

`obj` | An object of class `MSnSet` containing quantitative data.
`percent` | TRUE or FALSE. Default is FALSE..
`condition` | Method used to choose the lines to delete. Values are : "None", "EmptyLines", "WholeMatrix", "AllCond", "AtLeastOneCond"
`threshold` | An integer value of the threshold if percent is FALSE. Otherwise, a floating number between 0 and 1.

### 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 vector of indices that correspond to the lines to keep.

### Author(s)

Enora Fremy, Samuel Wieczorek

### Examples

    utils::data(Exp1_R25_pept, package='DAPARdata')
    keepThat <- mvFilterGetIndices(Exp1_R25_pept, condition = "WholeMatrix", threshold=2)
    keepThat <- mvFilterGetIndices(Exp1_R25_pept, condition = "EmptyLines")
    keepThat <- mvFilterGetIndices(Exp1_R25_pept, condition = "WholeMatrix", percent=TRUE, threshold=0.5)

[Package DAPAR version 1.22.9 Index]