This package provides functions to analyse missing value mechanisms in the context of bottom-up MS-based quantitative proteomics.
It allows estimating a mixture model of missing completely-at-random (MCAR) values and missing not-at-random (MNAR) values.
It also contains functions allowing the imputation of missing values under hypotheses of MCAR and/or MNAR values.
The main functions of this package are the
impute.mi (multiple imputation) and
impute.mix (imputation based on a decision rule). They can be used to impute matrices containing peptide intensities (as Maxquant outputs for instance). Missing values has to be indicated with NA and a log-2 transformation of the intensities has to be applied before using these functions.
Maintainer: Quentin Giai Gianetto <email@example.com>