MEDIPSroiSet-class: MEDIPSroiSet class and internal functions

In chavez-lab/MEDIPS: DNA IP-seq data analysis

Description

MEDIPSroiSet class is used in the MEDIPS library in order to store and extract objects and information of the specified regions of interest (ROI) from the input file as well as parameter settings specified during the workflow.

Objects from the Class

Objects of the classes contain information about the provided short reads, MeDIP raw/count signals, and further parameter settings. A MEDIPS ROI SET object is created by the MEDIPS.createROIset() function. According slots will be filled during the workflow.

Slots

genome_name:

Object of class "character" : the refernce genome

chr_names:

Object of class "character" : the names of the chromosomes included within the MEDIPS ROI SET

chr_lengths:

Object of class "numeric" : the lengths of the chromosomes included within the MEDIPS ROI SET

sample_name:

Object of class "character" : the name of the input file

path_name:

Object of class "character" : the path to the input file

number_regions:

Object of class "numeric" : the total number of included regions

genome_count:

Object of class "numeric" : the raw MeDIP-seq signals at the bins

extend:

Object of class "numeric" : the length of the reads after extension

shifted:

Object of class "numeric" : the number of bases by which the reads are shifted along the sequencing direction

uniq:

Object of class "logical" : determines if reads mapping to exactly the same genomic position should be replaced by only on representative

ROI:

Object of class "GRanges": the genomic positions of the regions of interest

bin_number:

Object of class "numeric": the number of bins per region

Methods

genome_name

signature(object = "MEDIPSroiSet"): extracts the reference genome of the MEDIPS ROI SET

bin_number

signature(object = "MEDIPSroiSet"): extracts the number of bins per ROI the bin_number slot of the MEDIPS ROI SET

chr_names

signature(object = "MEDIPSroiSet"): extracts the names of the chromosomes included within the MEDIPS ROI SET

chr_lengths

signature(object = "MEDIPSroiSet"): extracts the length of the chromosomes included within the MEDIPS ROI SET

sample_name

signature(object = "MEDIPSroiSet"): extracts the name of the input file

path_name

signature(object = "MEDIPSroiSet"): extracts the path to the input file

number_regions

signature(object = "MEDIPSroiSet"): extracts the total number of included regions

genome_count

signature(object = "MEDIPSroiSet"): extracts the raw MeDIP-Seq signals at the genomic bins

extend

signature(object = "MEDIPSroiSet"): extracts the number of bases by which the regions are extended

show

signature(object = "MEDIPSroiSet"): prints a summary of the MEDIPS SET object content

shifted

signature(object = "MEDIPSroiSet"): extracts the number of bases by which the regions are shifted

uniq

signature(object = "MEDIPSroiSet"): extracts the specified value for the uniq parameter

rois

signature(object = "MEDIPSroiSet"): extracts the GRange object containing the regions of interest

MEDIPS.calibrationCurve

signature(MSet = "MEDIPSroiSet", CSet="COUPLINGset"): internal function for calculating the calibration curve

MEDIPS.negBin

signature(MSet="MEDIPSroiSet", CSet="COUPLINGset"): internal function for calculating methylatiopn probabilities with respect to CpG density dependent negative binomial distributions

MEDIPS.pois

signature(MSet="MEDIPSroiSet", CSet="COUPLINGset"): internal function for calculating methylatiopn probabilities with respect to CpG density dependent poisson distributions

MEDIPS.rms

signature(MSet="MEDIPSroiSet", CSet="COUPLINGset"): internal function for calculating relative methylation scores

Author(s)

Lukas Chavez, Joern Dietrich

Examples

showClass("MEDIPSroiSet")

chavez-lab/MEDIPS documentation built on Feb. 17, 2021, 3:24 a.m.