mergeAllRDSFilesFromDirectory: Merge nucleosome information from all RDS files present in a...

In ArnaudDroitLab/RJMCMC: Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)

Description

Merge nucleosome information, from all RDS files present in a same directory, into one object of class "rjmcmcNucleosomesMerge".

Usage

mergeAllRDSFilesFromDirectory(directory)

Arguments

directory

a character, the name of the directory (relative or absolute path) containing RDS files. The RDS files must contain R object of class "rjmcmcNucleosomes" or "rjmcmcNucleosomesMerge".

Value

a list of class "rjmcmcNucleosomesMerge" containing:

• k a integer, the number of nucleosomes.

• mu a vector of numeric of length k, the positions of the nucleosomes.

• sigmaf a vector of numeric of length k, the variance of the forward reads for each nucleosome.

• sigmar a vector of numeric of length k, the variance of the reverse reads for each nucleosome.

• delta a vector of numeric of length k, the distance between the maxima of the forward and reverse reads position densities for each nucleosome.

Author(s)

Pascal Belleau, Astrid Deschênes

Examples

## Use a directory present in the RJMCMC package
directoryWithRDSFiles <- system.file("extdata", package = "RJMCMC")

## Merge nucleosomes info from RDS files present in directory
## It is assumed that all files present in the directory are nucleosomes
## result for the same chromosome
result <- mergeAllRDSFilesFromDirectory(directoryWithRDSFiles)

## Print the number and the position of the nucleosomes
result$k
result$mu

## Class of the output object
class(result)

ArnaudDroitLab/RJMCMC documentation built on May 5, 2019, 7:06 a.m.