Package: amanida 0.3.0

Maria Llambrich

amanida: Meta-Analysis for Non-Integral Data

Combination of results for meta-analysis using significance and effect size only. P-values and fold-change are combined to obtain a global significance on each metabolite. Produces a volcano plot summarising the relevant results from meta-analysis. Vote-counting reports for metabolites. And explore plot to detect discrepancies between studies at a first glance. Methodology is described in the Llambrich et al. (2021) <doi:10.1093/bioinformatics/btab591>.

Authors:Maria Llambrich [aut, cre], Eudald Correig [aut], Raquel Cumeras [aut]

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amanida.pdf |amanida.html✨
amanida/json (API)

# Install 'amanida' in R:

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

Bug tracker:https://github.com/mariallr/amanida/issues

Datasets:

sample_data - Example input data for the amanida function

On CRAN:

4.85 score 7 stars 7 scripts 349 downloads 10 exports 112 dependencies

Last updated 10 months agofrom:8eaf5d1afc. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 22 2024
R-4.5-win	NOTE	Oct 22 2024
R-4.5-linux	NOTE	Oct 22 2024
R-4.4-win	NOTE	Oct 22 2024
R-4.4-mac	NOTE	Oct 22 2024
R-4.3-win	NOTE	Oct 22 2024
R-4.3-mac	NOTE	Oct 22 2024

Exports:amanida_read amanida_report amanida_vote check_names compute_amanida explore_plot getsampleDB METAtables volcano_plot vote_plot

Dependencies:askpass backports base64enc bit bit64 blob broom bslib cachem callr cellranger cli clipr colorspace conflicted cpp11 crayon curl data.table data.tree DBI dbplyr digest dplyr dtplyr evaluate fansi farver fastmap fontawesome forcats fs gargle generics ggplot2 ggrepel glue googledrive googlesheets4 gtable haven highr hms htmltools httr ids isoband jquerylib jsonlite kableExtra knitr labeling lattice lifecycle lubridate magrittr MASS Matrix memoise mgcv mime modelr munsell nlme openssl pillar pkgconfig prettyunits processx progress ps purrr R6 ragg rappdirs RColorBrewer Rcpp readr readxl rematch rematch2 reprex rlang rmarkdown rstudioapi rvest sass scales selectr stringi stringr svglite sys systemfonts textshaping tibble tidyr tidyselect tidyverse timechange tinytex tzdb utf8 uuid vctrs viridisLite vroom webchem withr xfun xml2 yaml

amanida_UserGuide

Maria Llambrich ([email protected])

Rendered fromamanida_UserGuide.Rmdusingknitr::rmarkdownon Oct 22 2024.

Last update: 2024-01-25
Started: 2021-08-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
amanida	amanida-package amanida
Get nice colour-blind colours	amanida_palette
Import data	amanida_read
Report	amanida_report
Qualitative meta-analysis	amanida_vote
Amanida harmonization	check_names
Combine statistical results and compute vote-counting	compute_amanida
Plot for compounds divergence in reports	explore_plot
Function to sample data path	getsampleDB
An S4 class to return results from 'compute_amanida' or 'amanida_vote' function	METAtables METAtables-class
Example input data for the amanida function	sample_data
Volcano plot of combined results	volcano_plot
Bar-plot for compounds vote-counting	vote_plot