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]

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chemhelper.pdf |chemhelper.html✨
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 114 dependencies

Last updated 2 years agofrom:e51054c185. Checks:OK: 1 ERROR: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 05 2024
R-4.5-win	ERROR	Nov 05 2024
R-4.5-linux	ERROR	Nov 05 2024
R-4.4-win	ERROR	Nov 05 2024
R-4.4-mac	ERROR	Nov 05 2024
R-4.3-win	ERROR	Nov 05 2024
R-4.3-mac	ERROR	Nov 05 2024

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 broom bslib cachem calibrate cli clipr colorspace cpp11 crayon crosstalk curl data.table data.tree DelayedArray digest dplyr evaluate fansi farver fastmap fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggrepel glue gtable highr hms htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite knitr labeling later latex2exp lattice lazyeval lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime MultiAssayExperiment MultiDataSet munsell nlme openssl pillar pkgconfig plotly prettyunits progress promises purrr qqman R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown ropls rvest S4Arrays S4Vectors sass scales selectr SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vctrs viridisLite vroom webchem withr xfun xml2 XVector yaml zlibbioc

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