diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..0002c62 Binary files /dev/null and b/.DS_Store differ diff --git a/.Rbuildignore b/.Rbuildignore index e13c405..a8eff32 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,19 @@ ^.*\.Rproj$ ^\.Rproj\.user$ ^LICENSE\.md$ +^doc$ +^Meta$ +^\.git$ +^./.git/*$ +CHANGELOG.md +KinformR.Rproj +^.Rproj.user/*$ +.Rhistory +.flake8 +.gitignore +.ignore_spelling.txt +.lintr +.pre-commit-config.yaml +.Rproj.user +.git +.github \ No newline at end of file diff --git a/.gitignore b/.gitignore index 16b31c3..7a43b82 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ .ignore_spelling.txt .flake8 .lintr +/doc/ +/Meta/ diff --git a/DESCRIPTION b/DESCRIPTION index 9e59962..e3523cf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,9 +1,11 @@ Package: KinformR -Title: Relationship-informed pedigree and variant scoring +Title: Relationship-Informed Pedigree and Variant Scoring Version: 0.1.0 Authors@R: - person("Cameron", "Nugent", , "cam.nugent@sequencebio.com", role = c("aut", "cre"), + person("Cameron M.", "Nugent", , "cam.nugent@sequencebio.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1135-2605")) +Author: Cameron M. Nugent +Maintainer: Cameron M. Nugent Description: The KinformR R package is meant to aid in comparative evaluation of families and candidate variants in rare-variant association studies. The package can be used for @@ -20,4 +22,5 @@ VignetteBuilder: knitr Suggests: devtools, testthat, - knitr + knitr, + rmarkdown diff --git a/vignettes/KinformR-penetrance_and_ibd.Rmd b/vignettes/KinformR-penetrance_and_ibd.Rmd index 87ae310..869165a 100644 --- a/vignettes/KinformR-penetrance_and_ibd.Rmd +++ b/vignettes/KinformR-penetrance_and_ibd.Rmd @@ -3,7 +3,7 @@ title: "KinformR - penetrance and idb informed scoring of families" author: "Cameron M. Nugent" date: "`r format(Sys.time(), '%d %B, %Y')`" data: "`r Sys.Date()`" -output: pdf_document #rmarkdown::html_vignette # +output: rmarkdown::pdf_document # rmarkdown::html_vignette # pdf_document: df_print: kable vignette: > @@ -96,6 +96,7 @@ show(penetrance.df) ``` The output includes seven columns that with the following information: + |Output Column|Description| |---|---| |family|The family id.| diff --git a/vignettes/KinformR-variant_scoring.Rmd b/vignettes/KinformR-variant_scoring.Rmd index 1042fee..ae66954 100644 --- a/vignettes/KinformR-variant_scoring.Rmd +++ b/vignettes/KinformR-variant_scoring.Rmd @@ -3,7 +3,7 @@ title: "KinformR - pedigree-informed rare variant association scoring" author: "Cameron M. Nugent" date: "`r format(Sys.time(), '%d %B, %Y')`" data: "`r Sys.Date()`" -output: pdf_document #rmarkdown::html_vignette # +output: rmarkdown::pdf_document #rmarkdown::html_vignette # pdf_document: df_print: kable vignette: >