mvFilterGetIndices: 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", "wholeMatrix", "allCond", "atLeastOneCond"
th
An integer value of the threshold
Value
An vector of indices that correspond to the lines to keep.
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.