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base repository: GreenwoodLab/funtooNorm
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base: v0.99.0
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head repository: GreenwoodLab/funtooNorm
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compare: master
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9 changes: 9 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -1,2 +1,11 @@
^.*\.Rproj$
^\.Rproj\.user$
^\.travis\.yml$
^R/ReadFiles.R$
^funtooNorm_0\.99\.4\.tar\.gz$
.\.RData$
\.(PCR|PLS)\.pdf$
^funtooNorm_old\.Rnw$
^\.travis\.yml$
^\.gitignore$
^.git
9 changes: 7 additions & 2 deletions .gitignore
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@@ -1,6 +1,11 @@
.Rproj.user
.Rhistory
.RData
*.RData
funtooNorm.Rproj
.Rbuildignore
.gitignore
inst/doc
# files created during vignette building
vignettes/*
!vignettes/funtooNorm.Rnw
!vignettes/funtooNorm.pdf

29 changes: 29 additions & 0 deletions .travis.yml
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@@ -0,0 +1,29 @@
language: r
r:
- release
- devel
- bioc-devel
sudo: false
cache: packages

env:
- RGL_USE_NULL=TRUE

r_build_args: --compact-vignettes=gs+qpdf
r_check_args: --as-cran

bioc_packages:
- BiocStyle
- illuminaio
- minfi
- minfiData

r_binary_packages:
- knitr
- pls

notifications:
email:
- maxime.turgeon@mail.mcgill.ca
- kathleen.klein@mail.mcgill.ca

39 changes: 30 additions & 9 deletions DESCRIPTION
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@@ -1,14 +1,35 @@
Package: funtooNorm
Type: Package
Title: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Version: 0.99.0
Date: 2015-05-19
Author: Celia Greenwood <celia.greenwood@mcgill.ca>, Stepan Grinek <stepan.grinek@ladydavis.ca>
Maintainer: Stepan Grinek <stepan.grinek@ladydavis.ca>
Description: Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.
Version: 1.1.1
Date: 2017-09-19
Author: Celia Greenwood <celia.greenwood@mcgill.ca>,Stepan Grinek
<stepan.grinek@ladydavis.ca>, Maxime Turgeon <maxime.turgeon@mail.mcgill.ca>,
Kathleen Klein <kathleen.klein@mail.mcgill.ca>
Maintainer: Kathleen Klein <kathleen.klein@mail.mcgill.ca>
Description: Provides a function to normalize Illumina Infinium Human
Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell
type.
License: GPL-3
Imports: pls
Suggests: BiocStyle, illuminaio
Depends: R(>= 2.10.0)
Imports:
pls,
matrixStats,
minfi,
methods,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
GenomeInfoDb,
grDevices,
graphics,
stats
Suggests:
prettydoc,
minfiData,
knitr,
rmarkdown
Depends:
R(>= 3.4)
LazyData: true
biocViews: DNAMethylation, Preprocessing, Normalization
VignetteBuilder: knitr
biocViews: DNAMethylation, Preprocessing, Normalization
RoxygenNote: 6.0.1
32 changes: 30 additions & 2 deletions NAMESPACE
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@@ -1,2 +1,30 @@
import('pls')
export('funtoonorm', 'agreement')
# Generated by roxygen2: do not edit by hand

export(agreement)
export(fromGenStudFiles)
export(fromRGChannelSet)
export(funtooNorm)
export(getGRanges)
export(getNormBeta)
export(getNormM)
export(getRawBeta)
export(getSnpM)
export(plotValidationGraph)
exportClasses(SampleSet)
exportMethods(show)
import(IlluminaHumanMethylation450kanno.ilmn12.hg19)
import(IlluminaHumanMethylation450kmanifest)
import(methods)
importClassesFrom(minfi,IlluminaMethylationAnnotation)
importClassesFrom(minfi,RGChannelSet)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rainbow)
importFrom(graphics,layout)
importFrom(graphics,legend)
importFrom(graphics,matplot)
importFrom(graphics,par)
importFrom(graphics,plot.new)
importFrom(graphics,text)
importFrom(stats,predict)
importFrom(stats,start)
17 changes: 17 additions & 0 deletions NEWS
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@@ -9,3 +9,20 @@
}
}

\section{Version 0.99.1}{
\itemize{
\item Few corrections
}
}

\section{Version 0.99.4}{
\itemize{
\item New version from Raphael Poujol
}
}

\section{Version 0.99.5}{
\itemize{
\item Release to Bioconductor.
}
}
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