On Fri, Jan 13, 2017 at 10:52 PM Ricardo Wurmus <
address@hidden> wrote:
Ra <address@hidden> 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)))
+ (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
0001-gnu-Add-r-sva.patch