{"Package":"enviGCMS","Type":"Package","Title":"GC/LC-MS Data Analysis for Environmental Science","Version":"0.7.1","Authors@R":"c(person(given = \"Miao\", family = \"YU\",\nrole = c(\"aut\", \"cre\"),\nemail = \"yufreecas@gmail.com\",\ncomment = c(ORCID = \"0000-0002-2804-6014\")),\nperson(given = \"Thanh\", family = \"Wang\",\nrole = c(\"ctb\"),\nemail = \"Thanh.Wang@oru.se\",\ncomment = c(ORCID = \"0000-0002-5729-1908\")))","Description":"Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.","URL":"https://github.com/yufree/enviGCMS","BugReports":"https://github.com/yufree/enviGCMS/issues","License":"GPL-2","Encoding":"UTF-8","LazyData":"true","Suggests":"knitr, testthat, xcms, MSnbase, plotly, shiny, rmarkdown, DT,\ncrosstalk","VignetteBuilder":"knitr","biocViews":"","Depends":"R (>= 2.10)","Imports":"Rdisop, BiocParallel, grDevices, graphics, stats, utils,\nmethods, animation (>= 2.2.3), RColorBrewer, mixtools,\ndata.table, igraph","RoxygenNote":"7.2.3","NeedsCompilation":"no","Packaged":"2023-02-05 23:31:18 UTC; yufree","Author":"Miao YU [aut, cre] (),\nThanh Wang [ctb] ()","Maintainer":"Miao YU ","Repository":"CRAN","Date/Publication":"2023-02-06 08:42:34 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/enviGCMS_0.7.1.tar.gz","jsonAuthors":[{"name":"Miao YU","email":"yufreecas@gmail.com","maintainer":true},{"name":"Thanh Wang","email":"Thanh.Wang@oru.se","maintainer":false}],"readme":"enviGCMS: GC-MS Data Analysis for Environmental Science\n================\n\n[![CRAN status](http://www.r-pkg.org/badges/version/enviGCMS)](https://cran.r-project.org/package=enviGCMS) [![Download counter](http://cranlogs.r-pkg.org/badges/enviGCMS)](https://cran.r-project.org/package=enviGCMS) [![](https://cranlogs.r-pkg.org/badges/grand-total/enviGCMS)](https://cran.r-project.org/package=enviGCMS) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) [![Build status](https://api.travis-ci.org/yufree/enviGCMS.svg?branch=master)](https://travis-ci.org/yufree/enviGCMS)\n\n`enviGCMS` provides functions for GC/LC-MS data analysis for environmental sciences.\n\nInstallation\n------------\n\nYou can either use the stable version of `enviGCMS` from CRAN,\n\n``` {r}\ninstall.packages(\"enviGCMS\")\n```\n\nor the current development snapshot from this GitHub repository:\n\n``` {r}\nremotes::install_github(\"yufree/enviGCMS\")\n```\n\nUsage\n-----\n\nCheck this [vignette](http://yufree.github.io/enviGCMS/articles/GCMSDA.html) for Data analysis of GC-MS and LC-MS in Environmental Science.\n\nCheck this [vignette](http://yufree.github.io/enviGCMS/articles/PooledQC.html) for Pooled QC analysis in Environmental Science.\n\n- get the mean and RSD of one sample for 5 technique replicate\n\n~~~\n# enviGCMS use functions in xcms to import the data, just type the path to your single sample\ndata1 <- enviGCMS:::getmd(‘sample1-1’)\ndata2 <- enviGCMS:::getmd(‘sample1-2’)\ndata3 <- enviGCMS:::getmd(‘sample1-3’)\ndata4 <- enviGCMS:::getmd(‘sample1-4’)\ndata5 <- enviGCMS:::getmd(‘sample1-5’)\n~~~\n\n- get the mean\n\n~~~\ndata <- (data1+data2+data3+data4+data5)/5\n~~~\n\n- get the standard deviation\n\n~~~\ndatasd <- sqrt(((data1-data)^2+(data2-data)^2+(data3-data)^2+(data4-data)^2+(data5-data)^2)/4)\n~~~\n\n- get the RSD\n\n~~~\ndatabrsd <- datasd/data\n~~~\n\n- plot the smooth scatter\n\n~~~\nplotsms(datarsd)\n~~~\n\n- plot the heatmap\n\n~~~\nplotms(data)\n~~~\n\n- plot the mz-rt scatter plot\n\n~~~\nplotmz(data)\n~~~\n\n- plot the boundary model\n\n~~~\nfindline(data)\n~~~\n\nDetailed usage of those functions in Environmental analysis could be found in this [paper](https://www.sciencedirect.com/science/article/pii/S0039914016309298) and the vignettes in this package.\n","jobInfo":{"package":"enviGCMS","version":"0.7.1","parsingStatus":"success","parserVersion":2,"parsedAt":"2023-02-06T10:30:20+0000"}}

Description

Usage

Arguments