mvFilterGetIndices: Filter lines in the matrix of intensities w.r.t. some...
In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description Usage Arguments Details Value Author(s) Examples

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.

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

`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.

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.

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

Enora Fremy, Samuel Wieczorek

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)