[med-svn] [r-other-apmswapp] 09/12: Commit local changes
Andreas Tille
tille at debian.org
Fri Nov 10 12:26:39 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-other-apmswapp.
commit 9fa90f46288dcdaa33d48e22226146da5c874ce6
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 10 13:22:16 2017 +0100
Commit local changes
---
debian/changelog | 2 +-
debian/control | 26 +++++----
debian/patches/series | 1 +
debian/patches/uses_deseq2.patch | 111 +++++++++++++++++++++++++++++++++++++++
debian/rules | 5 +-
5 files changed, 128 insertions(+), 17 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 6058a1f..6ccb5b1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,4 +4,4 @@ r-other-apmswapp (1.0-1) UNRELEASED; urgency=low
TODO: http://www.bioconductor.org/packages/2.6/bioc/html/DESeq.html
-> r-bioc-deseq (seems to depend from locfit)
- -- Andreas Tille <tille at debian.org> Mon, 04 May 2015 10:49:06 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 04 Nov 2016 11:28:50 +0100
diff --git a/debian/control b/debian/control
index 40dd140..3198240 100644
--- a/debian/control
+++ b/debian/control
@@ -1,10 +1,10 @@
Source: r-other-apmswapp
-Section: science
+Section: gnu-r
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Build-Depends: debhelper (>= 9),
- cdbs,
+ dh-r,
r-base-dev,
r-cran-gtools,
r-bioc-edger,
@@ -12,22 +12,21 @@ Build-Depends: debhelper (>= 9),
r-bioc-multtest,
r-bioc-genefilter,
r-bioc-aroma.light,
- r-cran-seqinr
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-other-apmswapp/trunk/
+ r-bioc-deseq2,
+ r-cran-seqinr,
+ r-cran-foreign,
+ r-cran-nnet
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-other-apmswapp/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-other-apmswapp/trunk/
Homepage: http://sourceforge.net/projects/apmswapp/
Package: r-other-apmswapp
-Architecture: any
+Architecture: all
Depends: ${misc:Depends},
- r-cran-gtools,
- r-bioc-edger,
- r-bioc-limma,
- r-bioc-multtest,
- r-bioc-genefilter,
- r-bioc-aroma.light,
- r-cran-seqinr
+ ${R:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
Description: GNU R Pre- and Postprocessing For Affinity Purification Mass Spectrometry
The reliable detection of protein-protein-interactions by affinity
purification mass spectrometry (AP-MS) is a crucial stepping stone for
@@ -35,4 +34,3 @@ Description: GNU R Pre- and Postprocessing For Affinity Purification Mass Spectr
typical AP-MS experiment is to separate true interaction proteins from
contaminants by contrasting counts of proteins binding to specific baits
with counts of negative controls.
-
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..b1daabd
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+uses_deseq2.patch
diff --git a/debian/patches/uses_deseq2.patch b/debian/patches/uses_deseq2.patch
new file mode 100644
index 0000000..b26a665
--- /dev/null
+++ b/debian/patches/uses_deseq2.patch
@@ -0,0 +1,111 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 04 Nov 2016 11:28:50 +0100
+Description: No idea whether this makes sense but Debian has now DESeq2 - just
+ try whether this might work as well.
+
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -10,7 +10,7 @@ Description: apmsWAPP provides a complet
+ It comprises pre-processing, scoring and postprocessing of protein interactions.
+ A final list of interaction candidates is reported: it provides a ranking of the candidates according
+ to their p-values which allow estimating the number of false-positive interactions.
+-Depends: genefilter, seqinr, multtest, gtools, limma, edgeR, DESeq,
++Depends: genefilter, seqinr, multtest, gtools, limma, edgeR, DESeq2,
+ aroma.light
+ License: Review License
+ LazyLoad: yes
+--- a/R/Inttab_Norm.R
++++ b/R/Inttab_Norm.R
+@@ -2,14 +2,14 @@
+ # Input: - original interaction matrix (interaction table including zeros, raw discrete counts!)
+ # - baittable = classification of samples and controls
+ # - different normalization methods can be chosen in "norm":
+-# "sumtotal", "upperquartile", "DESeq", "TMM", "quantile"
++# "sumtotal", "upperquartile", "DESeq2", "TMM", "quantile"
+ # Output: normed interaction-matrix (normed count table), scaling factors
+
+-norm.inttable <- function( inttab.mat, baittab, norm = c("sumtotal", "upperquartile", "DESeq", "TMM", "quantile")) {
++norm.inttable <- function( inttab.mat, baittab, norm = c("sumtotal", "upperquartile", "DESeq2", "TMM", "quantile")) {
+
+ require(limma)
+ require(edgeR)
+-require(DESeq)
++require(DESeq2)
+ require(aroma.light)
+ norm <- match.arg(norm)
+
+@@ -50,8 +50,8 @@ inttab.norm[,setdiff(Tpos,zerocount)] <-
+ }
+
+
+-# "DESeq" - normalization method in the DESeq package (Anders et al. 2010):
+-if(norm=="DESeq") {
++# "DESeq2" - normalization method in the DESeq2 package (Anders et al. 2010):
++if(norm=="DESeq2") {
+ cds <- newCountDataSet( inttab.mat, baittab$V3) # build countDataSet
+
+ cds1 <- estimateSizeFactors( cds[ ,Cpos] )
+--- a/R/TSPM_apms.r
++++ b/R/TSPM_apms.r
+@@ -19,7 +19,7 @@
+ # - (filtered) (normalized) count matrix
+
+
+-tspm_apms <- function(counts, baittab, norm = c("none", "sumtotal", "upperquartile", "DESeq", "TMM", "quantile"),Filter=TRUE, filter.method= c("IQR", "overallVar", "noVar"), var.cutoff=NA, limit=0, adj.method=c("BH","WY")) {
++tspm_apms <- function(counts, baittab, norm = c("none", "sumtotal", "upperquartile", "DESeq2", "TMM", "quantile"),Filter=TRUE, filter.method= c("IQR", "overallVar", "noVar"), var.cutoff=NA, limit=0, adj.method=c("BH","WY")) {
+ require(multtest)
+ require(gtools)
+
+--- a/R/saint_permF.r
++++ b/R/saint_permF.r
+@@ -35,7 +35,7 @@
+
+
+
+-saint_permF <- function(file_baittable, file_inttable, prottable, norm = c("none", "sumtotal", "upperquartile", "DESeq", "TMM", "quantile"),Filter=TRUE, filter.method= c("IQR", "overallVar", "noVar"), var.cutoff=NA, limit=0, intern.norm=FALSE, saint.options="2000 10000 0 1 0") {
++saint_permF <- function(file_baittable, file_inttable, prottable, norm = c("none", "sumtotal", "upperquartile", "DESeq2", "TMM", "quantile"),Filter=TRUE, filter.method= c("IQR", "overallVar", "noVar"), var.cutoff=NA, limit=0, intern.norm=FALSE, saint.options="2000 10000 0 1 0") {
+ require(multtest)
+ require(gtools)
+
+--- a/man/norm.inttable.Rd
++++ b/man/norm.inttable.Rd
+@@ -8,7 +8,7 @@ Normalization of spectral count data
+ Normalization of spectral counts in bait and control samples based on an AP-MS experiment.
+ }
+ \usage{
+-norm.inttable(inttab.mat, baittab, norm = c("sumtotal", "upperquartile", "DESeq", "TMM", "quantile"))
++norm.inttable(inttab.mat, baittab, norm = c("sumtotal", "upperquartile", "DESeq2", "TMM", "quantile"))
+ }
+
+ \arguments{
+@@ -30,7 +30,7 @@ Five different normalization methods, ad
+ In the \sQuote{sumtotal} normalization counts are divided by the total number of counts in the sample.
+ The \sQuote{upperquartile} normalization corrects counts by dividing each count by the 75\% quantile of its sample counts.
+ The \sQuote{quantile} method equalizes the distributions of protein counts across all samples.
+-In the \sQuote{DESeq} approach by Anders and Huber (2010), counts are divided by the the median of the ratio of its count over its geometric mean across all samples.
++In the \sQuote{DESeq2} approach by Anders and Huber (2010), counts are divided by the the median of the ratio of its count over its geometric mean across all samples.
+ In the \sQuote{TMM} approach by Robinson and Oshlack (2010), a scaling factor is computed as the weighted mean of log ratios between chosen test and reference samples.
+
+ }
+--- a/man/saint_permF.Rd
++++ b/man/saint_permF.Rd
+@@ -7,7 +7,7 @@ Pre- and Postprocessing for AP-MS data a
+ A complete workflow for the identification of true interaction proteins based on AP-MS data, embedding the scoring method SAINT into a pre- and postprocessing framework.
+ }
+ \usage{
+-saint_permF(file_baittable, file_inttable, prottable, norm = c("none", "sumtotal", "upperquartile", "DESeq", "TMM", "quantile"), Filter = TRUE, filter.method = c("IQR", "overallVar", "noVar"), var.cutoff = NA, limit = 0, intern.norm = FALSE, saint.options = "2000 10000 0 1 0")
++saint_permF(file_baittable, file_inttable, prottable, norm = c("none", "sumtotal", "upperquartile", "DESeq2", "TMM", "quantile"), Filter = TRUE, filter.method = c("IQR", "overallVar", "noVar"), var.cutoff = NA, limit = 0, intern.norm = FALSE, saint.options = "2000 10000 0 1 0")
+ }
+ %- maybe also 'usage' for other objects documented here.
+ \arguments{
+--- a/man/tspm_apms.Rd
++++ b/man/tspm_apms.Rd
+@@ -8,7 +8,7 @@ A complete workflow for the analysis of
+
+ }
+ \usage{
+-tspm_apms(counts, baittab, norm = c("none", "sumtotal", "upperquartile", "DESeq", "TMM", "quantile"), Filter = TRUE, filter.method = c("IQR", "overallVar", "noVar"), var.cutoff = NA, limit = 0, adj.method = c("BH", "WY"))
++tspm_apms(counts, baittab, norm = c("none", "sumtotal", "upperquartile", "DESeq2", "TMM", "quantile"), Filter = TRUE, filter.method = c("IQR", "overallVar", "noVar"), var.cutoff = NA, limit = 0, adj.method = c("BH", "WY"))
+ }
+
+ \arguments{
diff --git a/debian/rules b/debian/rules
index a135b83..529c38a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,4 +1,5 @@
#!/usr/bin/make -f
-debRreposname := other
-include /usr/share/R/debian/r-cran.mk
+%:
+ dh $@ --buildsystem R
+
--
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