recoup_test_data: Reference and genomic sample regions for recoup testing

recoup_test_dataR Documentation

Reference and genomic sample regions for recoup testing

Description

The testing data package containes a small gene set, a design data frame, some genomic regions and an input object for testing of recoup with ChIP-Seq and RNA-Seq data. Specifically:

  • test.input: A small data set which contains 10000 reads from H4K20me1 ChIP-Seq data from WT adult mice and Set8 (Pr-Set7) KO mice. The tissue is liver.

  • test.genome: A small gene set (100 genes) and their coordinates from mouse mm9 chromosome 12.

  • test.design: A data frame containing the 100 above genes categorized according to expression and strand.

  • test.exons: A GRangesList containing the exons of the 100 above genes for use with recoup RNA-Seq mode.

Format

data.frame and list objects whose format is accepted by recoup.

Author(s)

Panagiotis Moulos

Source

Personal communication with the Talianids lab at BSRC 'Alexander Fleming'. Unpublished data.


pmoulos/recoup documentation built on March 14, 2024, 5:21 p.m.