Description Objects from the Class Slots Methods Author(s) Examples
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 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.
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
signature(object = "MEDIPSroiSet")
: extracts the reference genome of the MEDIPS ROI SET
signature(object = "MEDIPSroiSet")
: extracts the number of bins per ROI the bin_number slot of the MEDIPS ROI SET
signature(object = "MEDIPSroiSet")
: extracts the names of the chromosomes included within the MEDIPS ROI SET
signature(object = "MEDIPSroiSet")
: extracts the length of the chromosomes included within the MEDIPS ROI SET
signature(object = "MEDIPSroiSet")
: extracts the name of the input file
signature(object = "MEDIPSroiSet")
: extracts the path to the input file
signature(object = "MEDIPSroiSet")
: extracts the total number of included regions
signature(object = "MEDIPSroiSet")
: extracts the raw MeDIP-Seq signals at the genomic bins
signature(object = "MEDIPSroiSet")
: extracts the number of bases by which the regions are extended
signature(object = "MEDIPSroiSet")
: prints a summary of the MEDIPS SET object content
signature(object = "MEDIPSroiSet")
: extracts the number of bases by which the regions are shifted
signature(object = "MEDIPSroiSet")
: extracts the specified value for the uniq parameter
signature(object = "MEDIPSroiSet")
: extracts the GRange object containing the regions of interest
signature(MSet = "MEDIPSroiSet", CSet="COUPLINGset")
: internal function for calculating the calibration curve
signature(MSet="MEDIPSroiSet", CSet="COUPLINGset")
: internal function for calculating methylatiopn probabilities with respect to CpG density dependent negative binomial distributions
signature(MSet="MEDIPSroiSet", CSet="COUPLINGset")
: internal function for calculating methylatiopn probabilities with respect to CpG density dependent poisson distributions
signature(MSet="MEDIPSroiSet", CSet="COUPLINGset")
: internal function for calculating relative methylation scores
Lukas Chavez, Joern Dietrich
1 | showClass("MEDIPSroiSet")
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