README.md

hrm

Lifecycle:
stable R build
status Coverage
Status

Easily install, load and update an R package ecosystem for performing analyses of high resolution metabolomics data.

hrm packages include:

Installation

Install the hrm package from GitHub using:

remotes::install_github('jasenfinch/hrm')

Usage

Loading the hrm packages will load the included R packages.

library(hrm)
#> Warning in .recacheSubclasses(def@className, def, env): undefined subclass
#> "numericVector" of class "Mnumeric"; definition not updated
#> ── Attaching packages ───────────────────────────────────────────── hrm 0.9.1 ──
#> ✓ chunky           0.1.0   ✓ projecttemplates 0.5.1 
#> ✓ metaboData       0.6.2   ✓ grover           1.0.7 
#> ✓ binneR           2.6.0   ✓ metabolyseR      0.14.3
#> ✓ profilePro       0.7.0   ✓ mzAnnotation     1.7.5 
#> ✓ MFassign         0.7.10  ✓ construction     0.2.10
#> ✓ composition      0.1.4   ✓ riches           0.2.1 
#> ✓ metaboMisc       0.5.7   ✓ metaboWorkflows  0.9.0
#> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
#> ✓ tibble  3.1.5     ✓ dplyr   1.0.7
#> ✓ tidyr   1.1.4     ✓ stringr 1.4.0
#> ✓ readr   2.0.2     ✓ forcats 0.5.1
#> ✓ purrr   0.3.4
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> x dplyr::collect()    masks xcms::collect()
#> x dplyr::combine()    masks MSnbase::combine(), Biobase::combine(), BiocGenerics::combine()
#> x tidyr::expand()     masks S4Vectors::expand()
#> x dplyr::filter()     masks stats::filter()
#> x dplyr::first()      masks S4Vectors::first()
#> x dplyr::glimpse()    masks tibble::glimpse(), metaboWorkflows::glimpse()
#> x dplyr::groups()     masks xcms::groups()
#> x dplyr::lag()        masks stats::lag()
#> x ggplot2::Position() masks BiocGenerics::Position(), base::Position()
#> x purrr::reduce()     masks metaboMisc::reduce(), MSnbase::reduce()
#> x dplyr::rename()     masks S4Vectors::rename()

Alteratively, these packages can be loaded using the following, without loading the hrm package directly.

hrm::hrmAttach()

A vector of the current hrm packages can be found by:

hrmPackages()
#>  [1] "chunky"           "projecttemplates" "metaboData"       "grover"          
#>  [5] "binneR"           "metabolyseR"      "profilePro"       "mzAnnotation"    
#>  [9] "MFassign"         "construction"     "composition"      "riches"          
#> [13] "metaboMisc"       "metaboWorkflows"

hrm associated packages can be updated using:

hrmUpdate()


jasenfinch/hrm documentation built on Oct. 24, 2021, 10:48 a.m.