diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..d3ddafe --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,3 @@ +^renv$ +^renv\.lock$ +^LICENSE\.md$ diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..9210f9b --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,45 @@ +{ + "creators": [ + { + "orcid": "0000-0001-8141-7788", + "affiliation": "University of Kentucky", + "name": "Flight, Robert" + }, + { + "orcid": "0000-0003-3995-5368", + "affiliation": "University of Kentucky", + "name": "Moseley, Hunter" + }, + { + "affiliation": "University of Kentucky", + "name": "Bhatt, Praneeth" + } + ], + + "license": "CC-BY 4.0", + + "title": "Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values", + + "related_identifiers": [ + { + "scheme": "doi", + "identifier": "10.5281/zenodo.6311002", + "relation": "isSupplementedBy", + "resource_type": "software" + }, + { + "scheme": "doi", + "identifier": "10.5281/zenodo.10570255", + "relation": "isSupplementedBy", + "resource_type": "software" + }, + { + "scheme": "doi", + "identifier": "10.5281/zenodo.10570285", + "relation": "isSupplementedBy", + "resource_type": "software" + } + ] + + +} diff --git a/README.md b/README.md index eb4368d..fcc7be4 100644 --- a/README.md +++ b/README.md @@ -5,11 +5,12 @@ All the code for generating the manuscript: -Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values -Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley -[biorxiv](https://doi.org/10.1101/2022.02.24.481854) +Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values, Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley [biorxiv](https://doi.org/10.1101/2022.02.24.481854) is contained within this repository. -is contained within this repository. +## License + +The contents of this work are licensed under a CC-BY license. +If you use any content, you must give attribution to this original work. ## R Packages Needed @@ -36,6 +37,20 @@ install.packages("renv") renv::restore() ``` +The {ICIKendallTau} package on GitHub is now different than the one used for this manuscript, you should install the one archived on Zenodo (v 0.3.20). + +``` +wget https://zenodo.org/records/10580528/files/ICIKendallTau_0.3.20.tar.gz?download=1 --output-document=ICIKendallTau_0.3.20.tar.gz +tar -xzvf ICIKendallTau_0.3.20.tar.gz +cd ICIKendallTau +``` + +Then start an R session from within the directory, and install it. + +```r +remotes::install_local() +``` + ## Rerun All Underlying Analyses If you want to rerun everything from the beginning, you can do `tar_make()` on the project, and it should just run it. diff --git a/doc/ici_kt_manuscript.Rmd b/doc/ici_kt_manuscript.Rmd index 6662f10..a9a5e16 100644 --- a/doc/ici_kt_manuscript.Rmd +++ b/doc/ici_kt_manuscript.Rmd @@ -157,7 +157,7 @@ We examine the effect of missing values on various simulated and real data-sets, Given the detrimental effects of including outlier samples in differential analyses, we also evaluate the ability of ICI-Kt to capture sample-sample pairwise similarities and the determination of outlier samples prior to differential analyses. Finally, we examine how feature-feature networks derived from various feature-feature correlations change within annotations depending on the correlation method used. -All of the code used for this manuscript is available on zenodo [@flightManuscriptICIKendallTau2022]. +All of the code used for this manuscript is available on zenodo [@flightManuscriptICIKendallTau2024]. ## Methods @@ -257,7 +257,7 @@ In comparison to directly counting the concordant and discordant pairs, some of Therefore, we used 64-bit integers and floats where necessary in the *Rcpp* code. C++ (via *Rcpp* [@eddelbuettel_rcppseamless_2011; @eddelbuettel_seamlessbook_2013; @eddelbuettel_extendingrcpp_2018]) and R code implementations are in the src/kendallc.cpp and R/kendalltau.R files of the ICIKendallTau R package, hosted at https://github.com/MoseleyBioinformaticsLab/ICIKendallTau. -The version of the package used in this manuscript is available on zenodo [@flightICIKendallTau2022]. +The version of the package used in this manuscript is available on zenodo [@flightICIKendallTau2023]. When a large number of samples need to be compared, it may be useful to split the comparisons across compute instances (across hyperthreaded cores, physical cores, or physical compute nodes). The *furrr* R package makes the definition of compute clusters trivial [@vaughanFurrrApplyMapping2021]. @@ -696,4 +696,8 @@ The results shown here are in whole or part based upon data generated by the TCG This work was supported in part by grants NSF 2020026 (PI Moseley), NSF ACI1626364 (Griffioen, Moseley), P30 CA177558 (PI Evers) via the Markey Cancer Center Biostatistics and Bioinformatics Shared Resource Facility (MCC BB-SRF), P20 GM121327 (PD St. Clair), and P42 ES007380 (PI Pennell) via the Data Management and Analysis Core (DMAC). We are heavily indebted to the University of Kentucky Center for Computational Sciences (CCS) provided Kentucky Research Informatics Cloud (KyRIC), an NSF supported computational resource (NSF ACI1626364) for access to large virtual machines that allowed for methods development and the running of many of the larger datasets in this manuscript. +## Supplemental materials + +In addition to the over 30 supplemental figures and tables, the following Zenodo item includes all of the data and code used to generate results: https://zenodo.org/doi/10.5281/zenodo.6309187 + ## References diff --git a/doc/icikt_references.json b/doc/icikt_references.json index 37b89ae..c42a0ca 100644 --- a/doc/icikt_references.json +++ b/doc/icikt_references.json @@ -2044,7 +2044,7 @@ } }, { - "id": "flightICIKendallTau2022", + "id": "flightICIKendallTau2023", "type": "document", "abstract": "ICIKendallTau version used in the manuscript Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley", "title": "ICIKendallTau", @@ -2062,14 +2062,14 @@ "issued": { "date-parts": [ [ - "2022", - 2 + "2023", + 12 ] ] } }, { - "id": "flightManuscriptICIKendallTau2022", + "id": "flightManuscriptICIKendallTau2024", "type": "document", "title": "manuscript.ICIKendallTau", "URL": "https://dx.doi.org/10.5281/zenodo.6309187", @@ -2081,13 +2081,17 @@ { "family": "Moseley", "given": "Hunter N. B." + }, + { + "family": "Bhatt", + "given": "Praneeth S." } ], "issued": { "date-parts": [ [ - "2022", - 2 + "2024", + 1 ] ] }