syntheticNucleosomeReads: Simulated dataset of reads generated by 'nucleoSim' package...

In RJMCMCNucleosomes: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Description

A list of class "syntheticNucReads" which contains the information about synthetic reads related to nucleosomes. The datset has been created using a total of 300 well-positioned nucleosomes, 30 fuzzy nucleosomes with variance of reads following a Normal distribution.

Usage

data(syntheticNucleosomeReads)

Format

A list containing:

• call the called that generated the dataset.

• dataIP a data.frame with the chromosome name, the starting and ending positions and the direction of all forward and reverse reads for all well-positioned and fuzzy nucleosomes. Paired-end reads are identified with an unique id.

• wp a data.frame with the positions of all the well-positioned nucleosomes, as well as the number of paired-reads associated to each one.

• fuz a data.frame with the positions of all the fuzzy nucleosomes, as well as the number of paired-reads associated to each one.

• paired a data.frame with the starting and ending positions of the reads used to generate the paired-end reads. Paired-end reads are identified with an unique id.

Value

A list containing:

• call the called that generated the dataset.

• dataIP a data.frame with the chromosome name, the starting and ending positions and the direction of all forward and reverse reads for all well-positioned and fuzzy nucleosomes. Paired-end reads are identified with an unique id.

• wp a data.frame with the positions of all the well-positioned nucleosomes, as well as the number of paired-reads associated to each one.

• fuz a data.frame with the positions of all the fuzzy nucleosomes, as well as the number of paired-reads associated to each one.

• paired a data.frame with the starting and ending positions of the reads used to generate the paired-end reads. Paired-end reads are identified with an unique id.

RJMCMCNucleosomes documentation built on Nov. 8, 2020, 8:20 p.m.