XRanges: A simulated data set for CNV detection from NGS data.

In cn.mops: cn.mops - Mixture of Poissons for CNV detection in NGS data

Description

This data set gives the read counts of 40 samples in 5000 genomic locations. The rows correspond to genomic segments of 25kbp length and the columns to samples. An entry is the number of reads that map to the specific segment of the sample. The "GRanges" object contains the name of the reference sequence, start and end position of the genomic segments. The simulated data contains CNVs given in the CNVRanges object. It was generated using distributions of read counts as they appear in real sequencing experiments. CNVs were implanted under the assumption that the expected read count is linear dependent on the copy number (e.g. in a certain genomic we expect lambda reads for copy number 2, then we expect 2*lambda reads for copy number 4).

Usage

XRanges

Format

A GRanges object with 5000 rows and 40 value columns across 1 space.

Source

http://www.bioinf.jku.at/software/cnmops/cnmops.html.

References

Guenter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arne Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter. cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate. Nucleic Acids Research 2012 40(9); doi:10.1093/nar/gks003.

cn.mops documentation built on Nov. 8, 2020, 5:59 p.m.