ETn_example: ETn Recombination hotspots data

In marziacremona/IWTomics: Interval-Wise Testing for Omics Data

Description

Recombination hotspots data in the regions surrounding fixed ETns (elements of the Early Transposon family of active Endogenous Retroviruses in mouse) and in control regions.

Usage

data(ETn_example)

Format

ETn_example is an object of class "IWTomicsData", with two region datasets "ETn fixed" and "Control" with center alignment 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.

Value

"IWTomicsData" object.

Source

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.

Examples

data(ETn_example)
ETn_example

plot(ETn_example,type='boxplot')

marziacremona/IWTomics documentation built on May 21, 2019, 12:39 p.m.