[PATCH] gnu: Add r-sva

[PATCH] gnu: Add r-sva

[Ra]

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* gnu/packages/bioinformatics.scm (r-sva): New variable.
---
 gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index d82b6c0..c6acab1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,38 @@ immunoprecipitation and target enrichment on small
gene panels.  Thereby,
 CopywriteR constitutes a widely applicable alternative to available copy
 number detection tools.")
     (license license:gpl2)))
+
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha265
+        (base32
+         "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genefilter" ,r-genefilter)))
+    (home-page "http://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. Specifically,
+the sva package contains functions for the identifying and building
+surrogate variables for high-dimensional data sets. Surrogate variables
+are covariates constructed directly from high-dimensional data (like gene
+expression/RNA sequencing/methylation/brain imaging data) that can be used
+in subsequent analyses to adjust for unknown, unmodeled, or latent sources
+of noise. The sva package can be used to remove artifacts in three ways:
+1. identifying and estimating surrogate variables for unknown sources of
+variation in high-throughput experiments Leek and Storey 2007 PLoS
Genetics,
+ 2008 PNAS,2. directly removing known batch effects using ComBat
+Johnson et al. 2007 Biostatistics and 3. removing batch effects with known
+control probes Leek 2014 biorXiv. Removing batch effects and using
surrogate
+variables in differential expression analysis have been shown to reduce
+dependence, stabilize error rate estimates, and improve reproducibility,
+see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat.
Reviews Genetics.")
+    (license license:artistic2.0)))
--
1.9.1

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From 821e0f26e2ee8cb6213fe5920fcd71a7f1c64985 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Fri, 13 Jan 2017 20:38:25 +0100
Subject: [PATCH] gnu: Add r-sva

* gnu/packages/bioinformatics.scm (r-sva): New variable.
---
 gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d82b6c0..c6acab1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,38 @@ immunoprecipitation and target enrichment on small gene panels.  Thereby,
 CopywriteR constitutes a widely applicable alternative to available copy
 number detection tools.")
     (license license:gpl2)))
+
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha265
+        (base32
+         "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genefilter" ,r-genefilter)))
+    (home-page "http://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. Specifically,
+the sva package contains functions for the identifying and building
+surrogate variables for high-dimensional data sets. Surrogate variables
+are covariates constructed directly from high-dimensional data (like gene
+expression/RNA sequencing/methylation/brain imaging data) that can be used
+in subsequent analyses to adjust for unknown, unmodeled, or latent sources
+of noise. The sva package can be used to remove artifacts in three ways:
+1. identifying and estimating surrogate variables for unknown sources of
+variation in high-throughput experiments Leek and Storey 2007 PLoS Genetics,
+ 2008 PNAS,2. directly removing known batch effects using ComBat
+Johnson et al. 2007 Biostatistics and 3. removing batch effects with known
+control probes Leek 2014 biorXiv. Removing batch effects and using surrogate
+variables in differential expression analysis have been shown to reduce
+dependence, stabilize error rate estimates, and improve reproducibility,
+see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics.")
+    (license license:artistic2.0)))
-- 
1.9.1

Re: [PATCH] gnu: Add r-sva

[Ricardo Wurmus]

Ra <ilpuccio.febo@gmail.com> writes:

> * gnu/packages/bioinformatics.scm (r-sva): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
>  1 file changed, 35 insertions(+)

Thanks for the patch.  I tried to apply this but got this error:

    error: corrupt patch at line 12

Could you resend the patch please?

> +    (description
> +     "This package contains functions for removing batch effects and
> +other unwanted variation in high-throughput experiment. Specifically,
> +the sva package contains functions for the identifying and building
> +surrogate variables for high-dimensional data sets. Surrogate variables
> +are covariates constructed directly from high-dimensional data (like gene
> +expression/RNA sequencing/methylation/brain imaging data) that can be used
> +in subsequent analyses to adjust for unknown, unmodeled, or latent sources
> +of noise. The sva package can be used to remove artifacts in three ways:
> +1. identifying and estimating surrogate variables for unknown sources of
> +variation in high-throughput experiments Leek and Storey 2007 PLoS
> Genetics,
> + 2008 PNAS,2. directly removing known batch effects using ComBat
> +Johnson et al. 2007 Biostatistics and 3. removing batch effects with known
> +control probes Leek 2014 biorXiv. Removing batch effects and using
> surrogate
> +variables in differential expression analysis have been shown to reduce
> +dependence, stabilize error rate estimates, and improve reproducibility,
> +see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat.
> Reviews Genetics.")
> +    (license license:artistic2.0)))

Could you please shorten the description?  A paragraph or two would be
sufficient.  We also don’t need the references to publications.  If you
decide to keep (a shortened variant of) the enumeration, please use
texinfo syntax.

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
http://elephly.net

Re: [PATCH] gnu: Add r-sva

[Ra]

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Hi Ricardo,

On Fri, Jan 13, 2017 at 10:52 PM Ricardo Wurmus <rekado@elephly.net> wrote:

> Ra <ilpuccio.febo@gmail.com> writes:
>
> > * gnu/packages/bioinformatics.scm (r-sva): New variable.
> > ---
> >  gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++++
> >  1 file changed, 35 insertions(+)
>
> Thanks for the patch.  I tried to apply this but got this error:
>
>     error: corrupt patch at line 12
>
> Could you resend the patch please?
>
> > +    (description
> > +     "This package contains functions for removing batch effects and
> > +other unwanted variation in high-throughput experiment. Specifically,
> > +the sva package contains functions for the identifying and building
> > +surrogate variables for high-dimensional data sets. Surrogate variables
> > +are covariates constructed directly from high-dimensional data (like
> gene
> > +expression/RNA sequencing/methylation/brain imaging data) that can be
> used
> > +in subsequent analyses to adjust for unknown, unmodeled, or latent
> sources
> > +of noise. The sva package can be used to remove artifacts in three ways:
> > +1. identifying and estimating surrogate variables for unknown sources of
> > +variation in high-throughput experiments Leek and Storey 2007 PLoS
> > Genetics,
> > + 2008 PNAS,2. directly removing known batch effects using ComBat
> > +Johnson et al. 2007 Biostatistics and 3. removing batch effects with
> known
> > +control probes Leek 2014 biorXiv. Removing batch effects and using
> > surrogate
> > +variables in differential expression analysis have been shown to reduce
> > +dependence, stabilize error rate estimates, and improve reproducibility,
> > +see Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011
> Nat.
> > Reviews Genetics.")
> > +    (license license:artistic2.0)))
>
> Could you please shorten the description?  A paragraph or two would be
> sufficient.  We also don’t need the references to publications.  If you
> decide to keep (a shortened variant of) the enumeration, please use
> texinfo syntax.
>
>
follows the patch with the reduced description, sorry for the long version.
I do not know why you get the "corrupt" message, I hope that attaching the
patch file could solve the issue.



* gnu/packages/bioinformatics.scm (r-sva): New variable.
---
 gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index d82b6c0..867a72e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,29 @@ immunoprecipitation and target enrichment on small
gene panels.  Thereby,
 CopywriteR constitutes a widely applicable alternative to available copy
 number detection tools.")
     (license license:gpl2)))
+
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha256
+        (base32
+         "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genefilter" ,r-genefilter)))
+    (home-page "http://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. The package
+contains functions for identifying and building surrogate variables
+for high-dimensional data sets. Surrogate variables are covariates
+constructed directly from high-dimensional data like gene expression/RNA
+sequencing/methylation/brain imaging data that can be used in subsequent
+analyses to adjust for unknown, unmodeled, or latent sources of noise.")
+    (license license:artistic2.0)))
--
1.9.1

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[-- Attachment #2: 0001-gnu-Add-r-sva.patch --]
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From 959e9a997fc01598bdc18a76e2948b7b60bfc943 Mon Sep 17 00:00:00 2001
From: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
Date: Fri, 13 Jan 2017 20:38:25 +0100
Subject: [PATCH] gnu: Add r-sva

* gnu/packages/bioinformatics.scm (r-sva): New variable.
---
 gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d82b6c0..867a72e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7995,3 +7995,29 @@ immunoprecipitation and target enrichment on small gene panels.  Thereby,
 CopywriteR constitutes a widely applicable alternative to available copy
 number detection tools.")
     (license license:gpl2)))
+
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha256
+        (base32
+         "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genefilter" ,r-genefilter)))
+    (home-page "http://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and
+other unwanted variation in high-throughput experiment. The package
+contains functions for identifying and building surrogate variables 
+for high-dimensional data sets. Surrogate variables are covariates
+constructed directly from high-dimensional data like gene expression/RNA
+sequencing/methylation/brain imaging data that can be used in subsequent
+analyses to adjust for unknown, unmodeled, or latent sources of noise.")
+    (license license:artistic2.0)))
-- 
1.9.1

Re: [PATCH] gnu: Add r-sva

[Ricardo Wurmus]

Ra <ilpuccio.febo@gmail.com> writes:

> follows the patch with the reduced description, sorry for the long version.
> I do not know why you get the "corrupt" message, I hope that attaching the
> patch file could solve the issue.

The inline patch didn’t work, but the attached version was fine.  Don’t
know what went wrong here.  Thanks for your patience!

I made a few minor changes:

* added a trailing period to the commit summary line
* converted the description to use two spaced between sentences
* slightly reworded the second sentence

Thanks again for the patch!  I pushed it to master as dd42a330d.

I’m looking forward to more of your contributions to the statistics and
bioinformatics modules!

--
Ricardo

GPG: BCA6 89B6 3655 3801 C3C6  2150 197A 5888 235F ACAC
http://elephly.net