wrapper.impute.pa: Imputation of peptides having no values in a biological...

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

Imputation of peptides having no values in a biological condition.

Description

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

Usage

wrapper.impute.pa(obj = NULL, q.min = 0.025, na.type)

Arguments

obj	An object of class MSnSet.
q.min	Same as the function impute.pa in the package imp4p
na.type	A string which indicates the type of missing values to impute. Available values are: 'NA' (for both POV and MEC).

Value

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

Author(s)

Samuel Wieczorek

Examples

utils::data(Exp1_R25_pept, package='DAPARdata')
obj <- Exp1_R25_pept[1:10]
level <- obj@experimentData@other$typeOfData
metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
obj.imp.pov <- wrapper.impute.pa(obj, na.type = 'missing POV')

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.