In szymczak-lab/preprocessHighResMS: Preprocessing of spectra data from high resolution mass spectrometry

---

title: "preprocessHighResMS" output: github_document

---

knitr::opts_chunk$set(echo = TRUE)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

This R package implements preprocessing methods for mass spectrometry data generated with direct infusion high resolution technology (e.g. FT-ICR).

Installation

First install the dependencies from CRAN:

## install CRAN dependencies
cran.dep = c("enviPat",
             "FTICRMS",
             "plyr")

cran.dep.to.install = setdiff(cran.dep,
                     installed.packages()[, "Package"])

if (length(cran.dep.to.install) > 0) {
    install.packages(cran.dep.to.install)
}

Next install the dependencies from Bioconductor:

## install Bioconductor dependencies
bioc.dep = c("SummarizedExperiment",
             "xcms")

bioc.dep.to.install = setdiff(bioc.dep,
                              installed.packages()[, "Package"])

if (length(bioc.dep.to.install) > 0) {
    if (!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")

    BiocManager::install(bioc.dep.to.install)
}

Then install the most recent version of preprocessHighResMS from GitHub:

library(devtools)
install_github("szymczak-lab/preprocessHighResMS")

Usage

A detailed user guide is available as vignette.

szymczak-lab/preprocessHighResMS documentation built on Oct. 6, 2020, 12:50 a.m.