In lauzikaite/massFlowR: LC-MS Data Pre-Processing

Package: massFlowR
Authors: Elzbieta Lauzikaite
Date: r date()

BiocStyle::markdown() 
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}
## supressing progress bar
options(kpb.suppress_noninteractive = TRUE) 

## load libraries quietly to avoid printing messages in the vignette
suppressWarnings(library(massFlowR))
out_directory <- getwd()
url_p <- "https://htmlpreview.github.io/?https://github.com/lauzikaite/massFlowR/blob/master/vignettes/processing.html"
url_a <- "https://htmlpreview.github.io/?https://github.com/lauzikaite/massFlowR/blob/master/vignettes/annotation.html"

Overview

This documents provides an overview of the LC-MS data pre-processing with massFlowR.

massFlowR aligns and annotates structurally-related spectral peaks across LC-MS experiment samples. The pipeline consists of three stages:

• Processing of individual LC-MS samples
• Peak alignment across samples
• Post-alignment processing

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knitr::include_graphics("../man/figures/scheme.png")

Peak annotation

If in-house chemical reference database is available, feature table generated by the pipeline can be automatically annotated. For more details how to build a database file, see annotation using database).

See also

• Data processing
• Automatic peak annotation

lauzikaite/massFlowR documentation built on April 29, 2020, 9:45 a.m.