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, type, th)

Arguments

obj

An object of class MSnSet containing quantitative data.

type

Method used to choose the lines to delete. Values are : "None", "EmptyLines", "wholeMatrix", "allCond", "atLeastOneCond"

th

An integer value of the threshold

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)

Florence Combes, Samuel Wieczorek

Examples

require(DAPARdata)
data(Exp1_R25_pept)
mvFilterGetIndices(Exp1_R25_pept, "wholeMatrix", 2)

[Package DAPAR version 1.16.0 Index]