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Merged
CNuge merged 1 commit into from
Sep 5, 2025
Merged

Testing --as-cran-build #32

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16 changes: 16 additions & 0 deletions .Rbuildignore
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@@ -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
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -6,3 +6,5 @@
.ignore_spelling.txt
.flake8
.lintr
/doc/
/Meta/
9 changes: 6 additions & 3 deletions DESCRIPTION
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@@ -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 <cam.nugent@sequencebio.com>
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
Expand All @@ -20,4 +22,5 @@ VignetteBuilder: knitr
Suggests:
devtools,
testthat,
knitr
knitr,
rmarkdown
3 changes: 2 additions & 1 deletion vignettes/KinformR-penetrance_and_ibd.Rmd
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Expand Up @@ -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: >
Expand Down Expand Up @@ -96,6 +96,7 @@ show(penetrance.df)
```

The output includes seven columns that with the following information:

|Output Column|Description|
|---|---|
|family|The family id.|
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2 changes: 1 addition & 1 deletion vignettes/KinformR-variant_scoring.Rmd
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Expand Up @@ -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: >
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