changeset 12:af8c050ea4a9 draft

Uploaded 20170503
author fabio
date Wed, 03 May 2017 11:06:50 -0400
parents 3a56f8e72534
children ccc1889fa465
files ._ETn_example ._README.txt ._loadandplot.R ._loadandplot.xml ._plotwithscale.R ._plotwithscale.xml ._testandplot.R ._testandplot.xml ETn_example/._.DS_Store ETn_example/._Control.bed ETn_example/._ETn_fixed.bed ETn_example/._README.txt ETn_example/._Recombination_hotspots.txt ETn_example/._features.header ETn_example/._regions.header ETn_example/README ETn_example/README.txt README.txt example/._.DS_Store example/._Controls_regions.bed example/._Elements1_regions.bed example/._Elements2_regions.bed example/._Elements3_regions.bed example/._Feature1.bed example/._Feature2.bed example/._README.txt example/._features.header.bed.txt example/._regions.header.txt example/README example/README.txt
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--- a/ETn_example/README	Tue May 02 17:56:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
-In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
-fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
-of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
-used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
-sites).
-Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
-particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
-hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
-fraction of the 1-kb window that is covered by recombination hotspots
-
-Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
-Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
-endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
-12(6): 1-41.
-Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
-Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
-active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
-Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
-B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
-genome. Genetics. 191: 757-764.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ETn_example/README.txt	Wed May 03 11:06:50 2017 -0400
@@ -0,0 +1,21 @@
+This example contains two region datasets "ETn fixed", "Control" and one feature "Recombination hotspots content".
+In particular, the region dataset "ETn fixed" contains 1296 genomic regions of 64 kb surrounding
+fixed ETns elements (32-kb flanking sequences upstream and 32-kb flanking sequences downstream
+of each element). The region dataset "Control" contains 1142 regions of 64 kb without elements,
+used as control in the test. The regions are aligned around their center (i.e. around the ETn integration
+sites).
+Recombination hotspots measurements are associated to each "ETn fixed" and "Control" region. In
+particular, this feature is measured in 1-kb windows, so that each region is associated to a recombination
+hotspots curve made of 64 values. The measurement used is the feature content, i.e. the
+fraction of the 1-kb window that is covered by recombination hotspots
+
+Data have been collected and pre-processed by: R Campos-Sanchez, MA Cremona, A Pini, F
+Chiaromonte and KD Makova (2016). Integration and fixation preferences of human and mouse
+endogenous retroviruses uncovered with Functional Data Analysis. PLoS Computational Biology.
+12(6): 1-41.
+Fixed ETn positions come from: Y Zhang, IA Maksakova, L Gagnier, LN van de Lagemaat, DL
+Mager (2008). Genome-wide assessments reveal extremely high levels of polymorphism of two
+active families of mouse endogenous retroviral elements. PLoS Genetics. 4: e1000007.
+Recombination hotspots data come from: H Brunschwig, L Levi, E Ben-David, RW Williams,
+B Yakir, S Shifman (2012). Fine-scale maps of recombination rates and hotspots in the mouse
+genome. Genetics. 191: 757-764.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.txt	Wed May 03 11:06:50 2017 -0400
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+This tool requires the following dependencies:
+1. R (https://cran.r-project.org/)
+2. R/Bioconductor package IWTomics (https://bioconductor.org/packages/release/bioc/html/IWTomics.html)
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--- a/example/README	Tue May 02 17:56:05 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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-This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", 
-corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/example/README.txt	Wed May 03 11:06:50 2017 -0400
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+This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", 
+corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".