Package: chemhelper 0.0.0.9000

chemhelper: Helper Functions For Dealing With GCMS and LCMS data from IonAnalytics

Provides helper functions for parsing data exported from IonAnalytics, calculating retention indecies, and other miscelanous helper functions to assist in data wrangling.

Authors:Eric Scott [aut, cre]

chemhelper_0.0.0.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
chemhelper/json (API)

# Install 'chemhelper' in R:

install.packages('chemhelper', repos = c('https://aariq.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aariq/chemhelper/issues

On CRAN:

analytical-chemistry multivariate-analysis pls

2.41 score 4 stars 13 scripts 14 exports 112 dependencies

Last updated from:e51054c185. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	247
source / vignettes	OK	238
linux-release-x86_64	ERROR	265
macos-release-arm64	ERROR	168
macos-oldrel-arm64	ERROR	209
windows-devel	ERROR	207
windows-release	ERROR	201
windows-oldrel	ERROR	229
wasm-release	OK	139

Exports:calc_RI calc_RT chem_scale get_loadings get_modelinfo get_plotdata get_scores get_VIP plot_opls plot_oplsda plot_pca plot_pls plot_plsda read_IA

Dependencies:abind askpass backports base64enc Biobase BiocBaseUtils BiocGenerics bit bit64 blob broom bslib cachem calibrate cli clipr cpp11 crayon crosstalk curl data.table data.tree DBI DelayedArray digest dplyr evaluate farver fastmap fontawesome fs generics GenomicRanges ggplot2 ggrepel glue gtable highr hms hoardr htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling later latex2exp lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mime MultiAssayExperiment MultiDataSet openssl otel pillar pkgconfig plotly prettyunits progress promises purrr qqman R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown ropls RSQLite rvest S4Arrays S4Vectors S7 sass scales selectr Seqinfo SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite vroom webchem withr xfun xml2 XVector yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate Van Den Dool and Kratz Retention Indicies	calc_RI
Back-calculate Retention Times	calc_RT
Scaling Functions for Metabolomics	chem_scale
Get axis loadings from models created by 'ropls::opls()'	get_loadings
Retrieve model parameters from models created by 'ropls::opls()' For PCA, returns percent variance explained by each axis. For (o)PLS(-DA), returns variance explained by axes and cross-validation statistics.	get_modelinfo
Extract data for plotting (O)PLS(-DA) data with ggplot2	get_plotdata
Get axis scores from models created by 'ropls::opls()' Returns a dataframe of PC axis scores for PCA, predictive axis scores for PLS and PLS-DA, and predictive and orthogonal axis scores for OPLS and OPLS-DA models.	get_scores
Get VIP scores from PLS and OPLS models created by 'ropls::opls()'	get_VIP
Parse IonAnalytics CSV files	parse_IA
Plot OPLS regression models produced by 'ropls::opls()'	plot_opls
Plot OPLS-DA models produced by 'ropls::opls()'	plot_oplsda
Plot PCA models created by 'ropls::opls()'	plot_pca
Plot PLS regression models produced by 'ropls::opls()'	plot_pls
Plot PLS-DA models produced by 'ropls::opls()'	plot_plsda
Read IonAnalytics CSV files	read_IA
Calculate a single Van Den Dool and Kratz Retention Index	VDDK_RI
Calculate a single retention time given a Van Den Dool and Kratz RI	VDDK_RT