wrapper.dapar.impute.mi: Missing values imputation using the LSimpute algorithm.
In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description Usage Arguments Value Author(s) Examples

This method is a wrapper to the function impute.mi of the package imp4p adapted to an object of class MSnSet.

wrapper.dapar.impute.mi(
  obj,
  nb.iter = 3,
  nknn = 15,
  selec = 600,
  siz = 500,
  weight = 1,
  ind.comp = 1,
  progress.bar = FALSE,
  x.step.mod = 300,
  x.step.pi = 300,
  nb.rei = 100,
  method = 4,
  gridsize = 300,
  q = 0.95,
  q.min = 0,
  q.norm = 3,
  eps = 0,
  methodi = "slsa",
  lapala = TRUE,
  distribution = "unif"
)

`obj`	An object of class `MSnSet`.
`nb.iter`	Same as the function `mi.mix` in the package `imp4p`
`nknn`	Same as the function `mi.mix` in the package `imp4p`
`selec`	Same as the function `mi.mix` in the package `imp4p`
`siz`	Same as the function `mi.mix` in the package `imp4p`
`weight`	Same as the function `mi.mix` in the package `imp4p`
`ind.comp`	Same as the function `mi.mix` in the package `imp4p`
`progress.bar`	Same as the function `mi.mix` in the package `imp4p`
`x.step.mod`	Same as the function `estim.mix` in the package `imp4p`
`x.step.pi`	Same as the function `estim.mix` in the package `imp4p`
`nb.rei`	Same as the function `estim.mix` in the package `imp4p`
`method`	Same as the function `estim.mix` in the package `imp4p`
`gridsize`	Same as the function `estim.mix` in the package `imp4p`
`q`	Same as the function `mi.mix` in the package `imp4p`
`q.min`	Same as the function `impute.pa` in the package `imp4p`
`q.norm`	Same as the function `impute.pa` in the package `imp4p`
`eps`	Same as the function `impute.pa` in the package `imp4p`
`methodi`	Same as the function `mi.mix` in the package `imp4p`
`lapala`	xxxxxxxxxxx
`distribution`	The type of distribution used. Values are `unif` (default) or `beta`.

The exprs(obj) matrix with imputed values instead of missing values.

Samuel Wieczorek

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utils::data(Exp1_R25_pept, package='DAPARdata')
dat <- mvFilter(Exp1_R25_pept[1:1000], type="AllCond", th = 1)
dat <- wrapper.dapar.impute.mi(dat, nb.iter=1)