Mercurial > repos > fabio > iwtomics
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 |
| diffstat | 30 files changed, 26 insertions(+), 23 deletions(-) [+] |
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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 @@ -0,0 +1,3 @@ +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)
--- a/example/README Tue May 02 17:56:05 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -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 @@ -0,0 +1,2 @@ +This example contains simulated measurements of two different genomic features, "ftr1" and "ftr2", +corresponding to four different region datasets: "elem1", "elem2", "elem3" and "control".