README.md

In qianli10000/GMSimpute: Generalized Mass Spectrum Missing Peaks Abundance Imputation

GMSimpute

GMSimpute is an R package that implements the Two-Step Lasso (TS-Lasso) and compound minimum to recover the abundance of missing peaks in mass spectrum analysis. TS-Lasso is a label-free imputation method that handles various types of missing peaks simultaneously. This package provides the procedure to generate missing peaks (or data) for simulation study, as well as a tool to estimate and visualize the proportion of missing at random.

Functions

GMS.Lasso

Generalized Mass Spectrum missing peaks imputation with Two-Step Lasso as default algorithm

TS.Lasso

Two-Step Lasso for missing peaks' abundance imputation

missing.sim

A pipeline to generate different patterns and proportions of missing peaks for simulation study

MAR.est

A tool to estimate and visualize the proportion of random missing peaks (i.e. caused by preprocessing)

Install GMSimpute

Clone and download GMSimpute to a local folder 'path' as GTSimpute-master.zip.

install.packages("path/GMSimpute-master.zip", repos = NULL, type = "source")

qianli10000/GMSimpute documentation built on May 9, 2019, 5:59 a.m.