mvFilter: Filter lines in the matrix of intensities w.r.t. some...

In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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

mvFilter(obj, type, th, processText = NULL)

Arguments

obj	An object of class MSnSet containing quantitative data.
type	Method used to choose the lines to delete. Values are : "None", "WholeMatrix", "AllCond", "AtLeastOneCond"
th	An integer value of the threshold
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')
mvFilter(Exp1_R25_pept, "WholeMatrix", 2)

DAPAR documentation built on April 11, 2021, 6 p.m.