diff --git a/README.md b/README.md index afa1facc..00a59768 100644 --- a/README.md +++ b/README.md @@ -14,10 +14,9 @@ should also be useful more generally. The methods are based on a new model for sparse multiple regression, which we call the "Sum of Single Effects" (SuSiE) model. This model, -which will be described in a manuscript in preparation (Wang et al), -lends itself to a particularly simple and intuitive fitting procedure --- effectively a Bayesian modification of simple forward selection, -which we call "Iterative Bayesian Step-wise Selection". +which is described in [Wang et al. (2020)](https://doi.org/10.1111/rssb.12388), lends itself to a particularly simple and intuitive fitting +procedure -- effectively a Bayesian modification of simple forward +selection, which we call "Iterative Bayesian Step-wise Selection". The output of the fitting procedure is a number of "Credible Sets" (CSs), which are each designed to have high probability to contain a @@ -27,10 +26,12 @@ correlated" variables that are each associated with the response: you can be confident that one of the variables has a non-zero coefficient, but they are too correlated to be sure which one. -The package is developed by Gao Wang, Peter Carbonetto, Yuxin Zou, -Kaiqian Zhang, and Matthew Stephens from the +The package was initially developed by Gao Wang, Peter Carbonetto, +Yuxin Zou, Kaiqian Zhang, and Matthew Stephens from the [Stephens Lab](https://stephenslab.uchicago.edu) at the University of -Chicago. +Chicago. It was later extended with new methods and implementations by +Alexander McCreight from the [StatFunGen Lab](https://wanggroup.org/) at +Columbia University. Please [post issues](https://github.com/stephenslab/susieR/issues) to ask @@ -61,21 +62,42 @@ please visit https://stephenslab.github.io/susieR ## Citing this work If you find the `susieR` package or any of the source code in this -repository useful for your work, please cite: +repository useful for your work, please cite both: -> G. Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. (2020). A +> Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. (2020). A > simple new approach to variable selection in regression, with > application to genetic fine mapping. *Journal of the Royal > Statistical Society, Series B* **82**, 1273–1300. > https://doi.org/10.1111/rssb.12388 -If you use any of the summary data methods such as `susie_suff_stat` -or `susie_rss`, please also cite: +> McCreight, A., Cho, Y., Nachun, D., Li, R., Gan, H-Y., Stephens, +> M., Carbonetto, P., Denault, W.R.P. & Wang, G. (2025). SuSiE 2.0: +> improved methods and implementations for genetic fine-mapping and +> phenotype prediction. Submitting to *Genome Biology*. + +If you use any of the summary data methods such as `susie_ss` or +`susie_rss`, please also cite: > Zou, Y., Carbonetto, P., Wang, G. & Stephens, M. (2022). Fine-mapping > from summary data with the "Sum of Single Effects" model. *PLoS > Genetics* **18**, e1010299. https://doi.org/10.1371/journal.pgen.1010299 +If you use the Servin-Stephens prior on residual variance estimates +(`estimate_residual_method = "Servin_Stephens"`), please also cite: + +> Denault, W.R.P., Carbonetto, P., Li, R., Consortium, A.D.F.G., Wang, +> G. & Stephens, M. (2025). Accounting for uncertainty in residual +> variances improves calibration of the "Sum of Single Effects" model +> for small sample sizes. *bioRxiv*, 2025-05. Under review for *Nature +> Methods*. + +If you use infinitesimal effects modeling (`unmappable_effects = "inf"`), +please also cite: + +> Cui, R., Elzur, R.A., Kanai, M. et al. (2024). Improving fine-mapping +> by modeling infinitesimal effects. *Nature Genetics* **56**, 162–169. +> https://doi.org/10.1038/s41588-023-01597-3 + ## Developer notes diff --git a/inst/CITATION b/inst/CITATION index 735c07ed..c552176b 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,4 +1,4 @@ -citHeader("To cite the susieR package, please use:") +citHeader("To cite the susieR package, please use both:") bibentry(bibtype = "Article", title = paste("A simple new approach to variable selection in", @@ -6,26 +6,46 @@ bibentry(bibtype = "Article", "mapping"), author = c(person("Gao","Wang"), person("Abhishek","Sarkar"), - person("Peter","Carbonetto"), + person("Peter","Carbonetto"), person("Matthew","Stephens")), journal = "Journal of the Royal Statistical Society, Series B", year = "2020", volume = "82", pages = "1273-1300", - doi = "10.1101/501114", - textVersion = - paste("Gao Wang, Abhishek Sarkar, Peter Carbonetto and Matthew", - "Stephens (2020). A simple new approach to variable", - "selection in regression, with application to genetic", - "fine mapping. Journal of the Royal Statistical Society,", - "Series B, 82, 1273-1300, doi:10.1101/501114")) + doi = "10.1111/rssb.12388", + textVersion = + paste("Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. (2020).", + "A simple new approach to variable selection in regression,", + "with application to genetic fine mapping. Journal of the", + "Royal Statistical Society, Series B 82, 1273-1300.", + "https://doi.org/10.1111/rssb.12388")) + +bibentry(bibtype = "Article", + title = paste("SuSiE 2.0: improved methods and implementations for", + "genetic fine-mapping and phenotype prediction"), + author = c(person("Alexander", "McCreight"), + person("Yanghyeon", "Cho"), + person("Daniel", "Nachun"), + person("Ruixi", "Li"), + person("Hao-Yu", "Gan"), + person("Matthew", "Stephens"), + person("Peter", "Carbonetto"), + person("William", "R.P. Denault"), + person("Gao", "Wang")), + journal = "Submitting to Genome Biology", + year = "2025", + textVersion = + paste("McCreight, A., Cho, Y., Nachun, D., Li, R., Gan, H-Y., Stephens,", + "M., Carbonetto, P., Denault, W.R.P. & Wang, G. (2025). SuSiE 2.0:", + "improved methods and implementations for genetic fine-mapping and", + "phenotype prediction. Submitting to Genome Biology.")) bibentry(header = "If susie_suff_stat or susie_rss is used, please also cite:", bibtype = "Article", title = paste('Fine-mapping from summary data with the', '"Sum of Single Effects" model'), author = c(person("Yuxin","Zou"), - person("Peter","Carbonetto"), + person("Peter","Carbonetto"), person("Gao","Wang"), person("Matthew","Stephens")), journal = "PLoS Genetics", @@ -33,8 +53,49 @@ bibentry(header = "If susie_suff_stat or susie_rss is used, please also cite:", year = "2022", pages = "e1010299", doi = "10.1371/journal.pgen.1010299", - textVersion = - paste('Yuxin Zou, Peter Carbonetto, Gao Wang and Matthew Stephens', - '(2022). Fine-mapping from summary data with the "Sum of', - 'Single Effects" model. PLoS Genetics 18, e1010299', - 'doi:10.1371/journal.pgen.1010299')) + textVersion = + paste('Zou, Y., Carbonetto, P., Wang, G. & Stephens, M. (2022).', + 'Fine-mapping from summary data with the "Sum of Single', + 'Effects" model. PLoS Genetics 18, e1010299.', + 'https://doi.org/10.1371/journal.pgen.1010299')) + +bibentry(header = paste("If estimate_residual_method = 'Servin_Stephens' is used,", + "please also cite:"), + bibtype = "Article", + title = paste("Accounting for uncertainty in residual variances", + "improves calibration of the 'Sum of Single Effects'", + "model for small sample sizes"), + author = c(person("William", "R.P. Denault"), + person("Peter", "Carbonetto"), + person("Ruixi", "Li"), + person("A.D.F.G.", "Consortium"), + person("Gao", "Wang"), + person("Matthew", "Stephens")), + journal = "bioRxiv", + year = "2025", + note = "Under review for Nature Methods", + textVersion = + paste("Denault, W.R.P., Carbonetto, P., Li, R., Consortium, A.D.F.G.,", + "Wang, G. & Stephens, M. (2025). Accounting for uncertainty in", + "residual variances improves calibration of the 'Sum of Single", + "Effects' model for small sample sizes. bioRxiv, 2025-05.", + "Under review for Nature Methods.")) + +bibentry(header = paste("If unmappable_effects = 'inf' is used,", + "please also cite:"), + bibtype = "Article", + title = "Improving fine-mapping by modeling infinitesimal effects", + author = c(person("Rui", "Cui"), + person("R.A.", "Elzur"), + person("M.", "Kanai"), + person(c("et", "al."))), + journal = "Nature Genetics", + volume = "56", + year = "2024", + pages = "162-169", + doi = "10.1038/s41588-023-01597-3", + textVersion = + paste("Cui, R., Elzur, R.A., Kanai, M. et al. (2024).", + "Improving fine-mapping by modeling infinitesimal effects.", + "Nature Genetics 56, 162-169.", + "https://doi.org/10.1038/s41588-023-01597-3"))